cartVersion	cartVersion	cartVersion	cartVersion	0	0	0	0	0	0	0	0	0	0	0		cartVersion	cartVersion	cartVersion	0	cartVersion 0
intronEst	Spliced ESTs	psl est	Mouse ESTs That Have Been Spliced	1	0.5	0	0	0	127	127	127	1	0	0			<h2>Description</h2>\
\
<p>\
This track shows alignments between mouse expressed sequence tags\
(ESTs) in <a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">\
GenBank</a> and the genome that show signs of splicing when\
aligned against the genome. ESTs are single-read sequences, typically about\
500 bases in length, that usually represent fragments of transcribed genes.\
</p>\
\
<p>\
To be considered spliced, an EST must show\
evidence of at least one canonical intron (i.e., the genomic\
sequence between EST alignment blocks must be at least 32 bases in\
length and have GT/AG ends). By requiring splicing, the level\
of contamination in the EST databases is drastically reduced\
at the expense of eliminating many genuine 3' ESTs.\
For a display of all ESTs (including unspliced), see the\
mouse EST track.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track follows the display conventions for\
<a href="/goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank">\
PSL alignment tracks</A>. In dense display mode, darker shading\
indicates a larger number of aligned ESTs.\
</p>\
\
<p>\
The strand information (+/-) indicates the\
direction of the match between the EST and the matching\
genomic sequence.  It bears no relationship to the direction\
of transcription of the RNA with which it might be associated.\
</p>\
\
<p>\
The description page for this track has a filter that can be used to change\
the display mode, alter the color, and include/exclude a subset of items\
within the track. This may be helpful when many items are shown in the track\
display, especially when only some are relevant to the current task.\
</p>\
\
<p>\
To use the filter:\
<ol>\
<li>Type a term in one or more of the text boxes to filter the EST\
display. For example, to apply the filter to all ESTs expressed in a specific\
organ, type the name of the organ in the tissue box. To view the list of\
valid terms for each text box, consult the table in the Table Browser that\
corresponds to the factor on which you wish to filter. For example, the\
&quot;tissue&quot; table contains all the types of tissues that can be\
entered into the tissue text box. Multiple terms may be entered at once,\
separated by a space. Wildcards may also be used in the filter.</li>\
<li>If filtering on more than one value, choose the desired combination\
logic. If &quot;and&quot; is selected, only ESTs that match all filter\
criteria will be highlighted. If &quot;or&quot; is selected, ESTs that\
match any one of the filter criteria will be highlighted.</li>\
<li>Choose the color or display characteristic that should be used to\
highlight or include/exclude the filtered items. If &quot;exclude&quot; is\
chosen, the browser will not display ESTs that match the filter criteria.\
If &quot;include&quot; is selected, the browser will display only those\
ESTs that match the filter criteria.</li>\
</ol>\
</p>\
\
<p>\
This track may also be configured to display base labeling, a feature that\
allows the user to display all bases in the aligning sequence or only those\
that differ from the genomic sequence. For more information about this option,\
go to the\
<a href="/goldenPath/help/hgBaseLabel.html" target="_blank">\
Base Coloring for Alignment Tracks</a> page.\
Several types of alignment gap may also be colored;\
for more information, go to the\
<a href="/goldenPath/help/hgIndelDisplay.html" target="_blank">\
Alignment Insertion/Deletion Display Options</a> page.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
To make an EST, RNA is isolated from cells and reverse\
transcribed into cDNA.  Typically, the cDNA is cloned\
into a plasmid vector and a read is taken from the 5'\
and/or 3' primer.  For most &mdash; but not all &mdash; ESTs, the\
reverse transcription is primed by an oligo-dT, which\
hybridizes with the poly-A tail of mature mRNA. The\
reverse transcriptase may or may not make it to the 5'\
end of the mRNA,  which may or may not be degraded.\
</p>\
\
<p>\
In general, the 3' ESTs mark the end of transcription\
reasonably well, but the 5' ESTs may end at any point\
within the transcript.  Some of the newer cap-selected\
libraries cover transcription start reasonably well. Before the\
cap-selection techniques\
emerged, some projects used random rather than poly-A\
priming in an attempt to retrieve sequence distant from the\
3' end.  These projects were successful at this, but as\
a side effect also deposited sequences from unprocessed\
mRNA and perhaps even genomic sequences into the EST databases.\
Even outside of the random-primed projects, there is a\
degree of non-mRNA contamination. Because of this, a\
single unspliced EST should be viewed with considerable\
skepticism.\
</p>\
\
<p>\
To generate this track, mouse ESTs from GenBank were aligned\
against the genome using blat. Note that the maximum intron length\
allowed by blat is 750,000 bases, which may eliminate some ESTs with very\
long introns that might otherwise align. When a single\
EST aligned in multiple places, the alignment having the\
highest base identity was identified.  Only alignments having\
a base identity level within 0.5% of the best and at least 96% base identity\
with the genomic sequence are displayed in this track.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
This track was produced at UCSC from EST sequence data\
submitted to the international public sequence databases by\
scientists worldwide.\
</p>\
\
<h2>References</h2>\
<p>\
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.\
<a href="https://academic.oup.com/nar/article/41/D1/D36/1068219/GenBank" target="_blank">\
GenBank</a>.\
<em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D36-42.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23193287" target="_blank">23193287</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531190/" target="_blank">PMC3531190</a>\
</p>\
\
<P>\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
<A HREF="https://academic.oup.com/nar/article/32/suppl_1/D23/2505202"\
TARGET=_blank>GenBank: update</A>.\
<em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D23-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681350" target="_blank">14681350</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308779/" target="_blank">PMC308779</a>\
</p>\
\
<P>\
Kent WJ.\
<A HREF="https://genome.cshlp.org/content/12/4/656.abstract"\
TARGET=_blank>BLAT - the BLAST-like alignment tool</A>.\
<em>Genome Res</em>. 2002 Apr;12(4):656-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a>\
</p>\
	rna	1	baseColorUseSequence genbank\
group rna\
indelDoubleInsert on\
indelQueryInsert on\
intronGap 30\
longLabel Mouse ESTs That Have Been Spliced\
maxItems 300\
priority 0.5\
shortLabel Spliced ESTs\
showDiffBasesAllScales .\
spectrum on\
track intronEst\
type psl est\
visibility dense\

chainRn4	Rat Chain	chain rn4	Rat (Nov. 2004 (Baylor 3.4/rn4)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of rat (Nov. 2004 (Baylor 3.4/rn4)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
rat and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
rat assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best rat/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The rat sequence used in this annotation is from\
the Nov. 2004 (Baylor 3.4/rn4) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the rat/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single rat chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>56</TD><TD>-109</TD><TD>-45</TD><TD>-137</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-109</TD><TD>100</TD><TD>-103</TD><TD>-45</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-45</TD><TD>-103</TD><TD>100</TD><TD>-109</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-137</TD><TD>-45</TD><TD>-109</TD><TD>56</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Rat (Nov. 2004 (Baylor 3.4/rn4)) Chained Alignments\
parent chainNetRn4Viewchain\
shortLabel Rat Chain\
subGroups view=chain\
track chainRn4\
type chain rn4\

chainBraFlo1	Lancelet Chain	chain braFlo1	Lancelet (Mar. 2006 (JGI 1.0/braFlo1)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of lancelet (Mar. 2006 (JGI 1.0/braFlo1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
lancelet and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
lancelet assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best lancelet/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The lancelet sequence used in this annotation is from\
the Mar. 2006 (JGI 1.0/braFlo1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the lancelet/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single lancelet chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Lancelet (Mar. 2006 (JGI 1.0/braFlo1)) Chained Alignments\
parent chainNetBraFlo1Viewchain\
shortLabel Lancelet Chain\
subGroups view=chain\
track chainBraFlo1\
type chain braFlo1\

chainOryLat2	Medaka Chain	chain oryLat2	Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
medaka and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
medaka assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best medaka/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The medaka sequence used in this annotation is from\
the Oct. 2005 (NIG/UT MEDAKA1/oryLat2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the medaka/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single medaka chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) Chained Alignments\
otherDb oryLat2\
parent chainNetOryLat2Viewchain\
shortLabel Medaka Chain\
subGroups view=chain\
track chainOryLat2\
type chain oryLat2\

chainLoxAfr3	Elephant Chain	chain loxAfr3	Elephant (Jul. 2009 (Broad/loxAfr3)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of elephant (Jul. 2009 (Broad/loxAfr3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
elephant and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
elephant assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best elephant/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The elephant sequence used in this annotation is from\
the Jul. 2009 (Broad/loxAfr3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the elephant/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single elephant chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Elephant (Jul. 2009 (Broad/loxAfr3)) Chained Alignments\
parent chainNetLoxAfr3Viewchain\
shortLabel Elephant Chain\
subGroups view=chain\
track chainLoxAfr3\
type chain loxAfr3\

chainEquCab2	Horse Chain	chain equCab2	Horse (Sep. 2007 (Broad/equCab2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of horse (Sep. 2007 (Broad/equCab2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
horse and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
horse assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best horse/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The horse sequence used in this annotation is from\
the Sep. 2007 (Broad/equCab2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the horse/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single horse chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Horse (Sep. 2007 (Broad/equCab2)) Chained Alignments\
parent chainNetEquCab2Viewchain\
shortLabel Horse Chain\
subGroups view=chain\
track chainEquCab2\
type chain equCab2\

chainCavPor3	Guinea pig Chain	chain cavPor3	Guinea pig (Feb. 2008 (Broad/cavPor3)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of guinea pig (Feb. 2008 (Broad/cavPor3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
guinea pig and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
guinea pig assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best guinea pig/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The guinea pig sequence used in this annotation is from\
the Feb. 2008 (Broad/cavPor3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the guinea pig/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single guinea pig chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Guinea pig (Feb. 2008 (Broad/cavPor3)) Chained Alignments\
parent chainNetCavPor3Viewchain\
shortLabel Guinea pig Chain\
subGroups view=chain\
track chainCavPor3\
type chain cavPor3\

chainRheMac2	Rhesus Chain	chain rheMac2	Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
rhesus and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
rhesus assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best rhesus/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The rhesus sequence used in this annotation is from\
the Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the rhesus/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single rhesus chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) Chained Alignments\
parent chainNetRheMac2Viewchain\
shortLabel Rhesus Chain\
subGroups view=chain\
track chainRheMac2\
type chain rheMac2\

chainAilMel1	Panda Chain	chain ailMel1	Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
panda and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
panda assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best panda/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The panda sequence used in this annotation is from\
the Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the panda/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single panda chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) Chained Alignments\
parent chainNetAilMel1Viewchain\
shortLabel Panda Chain\
subGroups view=chain\
track chainAilMel1\
type chain ailMel1\

chainGalGal3	Chicken Chain	chain galGal3	Chicken (May 2006 (WUGSC 2.1/galGal3)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of chicken (May 2006 (WUGSC 2.1/galGal3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
chicken and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
chicken assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best chicken/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The chicken sequence used in this annotation is from\
the May 2006 (WUGSC 2.1/galGal3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the chicken/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single chicken chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Chicken (May 2006 (WUGSC 2.1/galGal3)) Chained Alignments\
parent chainNetGalGal3Viewchain\
shortLabel Chicken Chain\
subGroups view=chain\
track chainGalGal3\
type chain galGal3\

chainDanRer7	Zebrafish Chain	chain danRer7	Zebrafish (Jul. 2010 (Zv9/danRer7)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of zebrafish (Jul. 2010 (Zv9/danRer7)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
zebrafish and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
zebrafish assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best zebrafish/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The zebrafish sequence used in this annotation is from\
the Jul. 2010 (Zv9/danRer7) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the zebrafish/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single zebrafish chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Zebrafish (Jul. 2010 (Zv9/danRer7)) Chained Alignments\
parent chainNetDanRer7Viewchain\
shortLabel Zebrafish Chain\
subGroups view=chain\
track chainDanRer7\
type chain danRer7\

chainAnoCar2	Lizard Chain	chain anoCar2	Lizard (May 2010 (Broad AnoCar2.0/anoCar2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of lizard (May 2010 (Broad AnoCar2.0/anoCar2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
lizard and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
lizard assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best lizard/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The lizard sequence used in this annotation is from\
the May 2010 (Broad AnoCar2.0/anoCar2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the lizard/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single lizard chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Lizard (May 2010 (Broad AnoCar2.0/anoCar2)) Chained Alignments\
parent chainNetAnoCar2Viewchain\
shortLabel Lizard Chain\
subGroups view=chain\
track chainAnoCar2\
type chain anoCar2\

chainCanFam2	Dog Chain	chain canFam2	Dog (May 2005 (Broad/canFam2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of dog (May 2005 (Broad/canFam2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
dog and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
dog assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best dog/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The dog sequence used in this annotation is from\
the May 2005 (Broad/canFam2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the dog/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single dog chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Dog (May 2005 (Broad/canFam2)) Chained Alignments\
parent chainNetCanFam2Viewchain\
shortLabel Dog Chain\
subGroups view=chain\
track chainCanFam2\
type chain canFam2\

chainMelGal1	Turkey Chain	chain melGal1	Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
turkey and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
turkey assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best turkey/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The turkey sequence used in this annotation is from\
the Dec. 2009 (TGC Turkey_2.01/melGal1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the turkey/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single turkey chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) Chained Alignments\
parent chainNetMelGal1Viewchain\
shortLabel Turkey Chain\
subGroups view=chain\
track chainMelGal1\
type chain melGal1\

chainOviAri1	Sheep Chain	chain oviAri1	Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
sheep and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
sheep assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best sheep/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The sheep sequence used in this annotation is from\
the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the sheep/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single sheep chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) Chained Alignments\
parent chainNetOviAri1Viewchain\
shortLabel Sheep Chain\
subGroups view=chain\
track chainOviAri1\
type chain oviAri1\

chainGasAcu1	Stickleback Chain	chain gasAcu1	Stickleback (Feb. 2006 (Broad/gasAcu1)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of stickleback (Feb. 2006 (Broad/gasAcu1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
stickleback and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
stickleback assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best stickleback/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The stickleback sequence used in this annotation is from\
the Feb. 2006 (Broad/gasAcu1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the stickleback/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single stickleback chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Stickleback (Feb. 2006 (Broad/gasAcu1)) Chained Alignments\
parent chainNetGasAcu1Viewchain\
shortLabel Stickleback Chain\
subGroups view=chain\
track chainGasAcu1\
type chain gasAcu1\

chainXenTro3	X. tropicalis Chain	chain xenTro3	X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
X. tropicalis and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
X. tropicalis assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best X. tropicalis/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The X. tropicalis sequence used in this annotation is from\
the Nov. 2009 (JGI 4.2/xenTro3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the X. tropicalis/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single X. tropicalis chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) Chained Alignments\
parent chainNetXenTro3Viewchain\
shortLabel X. tropicalis Chain\
subGroups view=chain\
track chainXenTro3\
type chain xenTro3\

chainFelCat4	Cat Chain	chain felCat4	Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
cat and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
cat assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best cat/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The cat sequence used in this annotation is from\
the Dec. 2008 (NHGRI/GTB V17e/felCat4) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the cat/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single cat chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) Chained Alignments\
parent chainNetFelCat4Viewchain\
shortLabel Cat Chain\
subGroups view=chain\
track chainFelCat4\
type chain felCat4\

chainMonDom5	Opossum Chain	chain monDom5	Opossum (Oct. 2006 (Broad/monDom5)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of opossum (Oct. 2006 (Broad/monDom5)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
opossum and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
opossum assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best opossum/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The opossum sequence used in this annotation is from\
the Oct. 2006 (Broad/monDom5) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the opossum/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single opossum chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Opossum (Oct. 2006 (Broad/monDom5)) Chained Alignments\
parent chainNetMonDom5Viewchain\
shortLabel Opossum Chain\
subGroups view=chain\
track chainMonDom5\
type chain monDom5\

chainPetMar1	Lamprey Chain	chain petMar1	Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
lamprey and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
lamprey assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best lamprey/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The lamprey sequence used in this annotation is from\
the Mar. 2007 (WUGSC 3.0/petMar1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the lamprey/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single lamprey chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) Chained Alignments\
parent chainNetPetMar1Viewchain\
shortLabel Lamprey Chain\
subGroups view=chain\
track chainPetMar1\
type chain petMar1\

chainHg19	Human Chain	chain hg19	Human (Feb. 2009 (GRCh37/hg19)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
human and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
human assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best human/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The human sequence used in this annotation is from\
the Feb. 2009 (GRCh37/hg19) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the human/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single human chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Human (Feb. 2009 (GRCh37/hg19)) Chained Alignments\
parent chainNetHg19Viewchain\
shortLabel Human Chain\
subGroups view=chain\
track chainHg19\
type chain hg19\

chainOrnAna1	Platypus Chain	chain ornAna1	Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
platypus and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
platypus assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best platypus/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The platypus sequence used in this annotation is from\
the Mar. 2007 (WUGSC 5.0.1/ornAna1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the platypus/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single platypus chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Chained Alignments\
parent chainNetOrnAna1Viewchain\
shortLabel Platypus Chain\
subGroups view=chain\
track chainOrnAna1\
type chain ornAna1\

chainFr2	Fugu Chain	chain fr2	Fugu (Oct. 2004 (JGI 4.0/fr2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of fugu (Oct. 2004 (JGI 4.0/fr2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
fugu and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
fugu assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best fugu/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The fugu sequence used in this annotation is from\
the Oct. 2004 (JGI 4.0/fr2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the fugu/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single fugu chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Fugu (Oct. 2004 (JGI 4.0/fr2)) Chained Alignments\
parent chainNetFr2Viewchain\
shortLabel Fugu Chain\
subGroups view=chain\
track chainFr2\
type chain fr2\

chainCalJac3	Marmoset Chain	chain calJac3	Marmoset (March 2009 (WUGSC 3.2/calJac3)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of marmoset (March 2009 (WUGSC 3.2/calJac3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
marmoset and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
marmoset assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best marmoset/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The marmoset sequence used in this annotation is from\
the March 2009 (WUGSC 3.2/calJac3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the marmoset/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single marmoset chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Marmoset (March 2009 (WUGSC 3.2/calJac3)) Chained Alignments\
parent chainNetCalJac3Viewchain\
shortLabel Marmoset Chain\
subGroups view=chain\
track chainCalJac3\
type chain calJac3\

chainOryCun2	Rabbit Chain	chain oryCun2	Rabbit (Apr. 2009 (Broad/oryCun2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of rabbit (Apr. 2009 (Broad/oryCun2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
rabbit and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
rabbit assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best rabbit/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The rabbit sequence used in this annotation is from\
the Apr. 2009 (Broad/oryCun2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the rabbit/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single rabbit chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Rabbit (Apr. 2009 (Broad/oryCun2)) Chained Alignments\
parent chainNetOryCun2Viewchain\
shortLabel Rabbit Chain\
subGroups view=chain\
track chainOryCun2\
type chain oryCun2\

chainTetNig2	Tetraodon Chain	chain tetNig2	Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
tetraodon and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
tetraodon assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best tetraodon/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The tetraodon sequence used in this annotation is from\
the Mar. 2007 (Genoscope 8.0/tetNig2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the tetraodon/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single tetraodon chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Chained Alignments\
parent chainNetTetNig2Viewchain\
shortLabel Tetraodon Chain\
subGroups view=chain\
track chainTetNig2\
type chain tetNig2\

chainPanTro3	Chimp Chain	chain panTro3	Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
chimp and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
chimp assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best chimp/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The chimp sequence used in this annotation is from\
the Oct. 2010 (CGSC 2.1.3/panTro3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the chimp/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single chimp chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) Chained Alignments\
parent chainNetPanTro3Viewchain\
shortLabel Chimp Chain\
subGroups view=chain\
track chainPanTro3\
type chain panTro3\

chainBosTau6	Cow Chain	chain bosTau6	Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
cow and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
cow assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best cow/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The cow sequence used in this annotation is from\
the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the cow/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single cow chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) Chained Alignments\
parent chainNetBosTau6Viewchain\
shortLabel Cow Chain\
subGroups view=chain\
track chainBosTau6\
type chain bosTau6\

chainSusScr2	Pig Chain	chain susScr2	Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
pig and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
pig assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best pig/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The pig sequence used in this annotation is from\
the Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the pig/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single pig chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) Chained Alignments\
parent chainNetSusScr2Viewchain\
shortLabel Pig Chain\
subGroups view=chain\
track chainSusScr2\
type chain susScr2\

chainPonAbe2	Orangutan Chain	chain ponAbe2	Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Chained Alignments	3	1	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
orangutan and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
orangutan assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best orangutan/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The orangutan sequence used in this annotation is from\
the July 2007 (WUGSC 2.0.2/ponAbe2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the orangutan/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single orangutan chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	html chainNet\
longLabel Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Chained Alignments\
parent chainNetPonAbe2Viewchain\
shortLabel Orangutan Chain\
subGroups view=chain\
track chainPonAbe2\
type chain ponAbe2\

wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hAlnRep1	10T1/2 Fibc Aln	bam	10T1/2 Fibrocyte 60 h RNA-seq Alignments from ENCODE/Caltech	0	1	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel 10T1/2 Fibrocyte 60 h RNA-seq Alignments from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewAlignments off\
shortLabel 10T1/2 Fibc Aln\
subGroups view=Alignments cellType=cell10T12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=E2P60H rep=rep1\
track wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hAlnRep1\
type bam\

wgEncodeUwDnase3134RiiiMImmortalHotspotsRep1	3134 H 1	broadPeak	3134 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	1	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel 3134 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots\
shortLabel 3134 H 1\
subGroups view=Hotspots age=IMMORTAL cellType=A13134 sex=M strain=RIII rep=rep1 treatment=zNONE\
track wgEncodeUwDnase3134RiiiMImmortalHotspotsRep1\
type broadPeak\

wgEncodeUwDgf3134RiiiMImmortalHotspotsRep1	3134 Immt H	broadPeak	3134 Immortal RIII DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	1	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel 3134 Immortal RIII DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel 3134 Immt H\
subGroups view=Hotspots age=IMMORTAL cellType=Cel3134 strain=RIII treatment=NONE rep=rep1\
track wgEncodeUwDgf3134RiiiMImmortalHotspotsRep1\
type broadPeak\

wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep1	A20 A 1	bam	A20 Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW	0	1	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel A20 Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel A20 A 1\
subGroups view=Alignments age=IMMORTAL cellType=A20 localization=CELL rnaExtract=POLYA sex=M strain=BALBCANN rep=rep1\
track wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep1\
type bam\

wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep1V2	Adrenal Aln 1	bam	Adrenal A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	1	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Adrenal A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Adrenal Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=ADRENAL rep=rep1\
track wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep1V2\
type bam\

agilentCgh1x1m	Ag CGH 1x1M	bed 4 .	Agilent SurePrint G3 Mouse CGH Microarray 1x1M AMADID 027414	0	1	0	128	0	127	191	127	0	0	0				varRep	1	color 0,128,0\
longLabel Agilent SurePrint G3 Mouse CGH Microarray 1x1M AMADID 027414\
nextItemButton off\
noScoreFilter .\
parent genotypeArrays\
priority 1\
shortLabel Ag CGH 1x1M\
track agilentCgh1x1m\
type bed 4 .\

cons30wayViewphyloP	Basewise Conservation (phyloP)	bed 4	30-Way Multiz Alignment & Conservation	2	1	0	0	0	127	127	127	0	0	0				compGeno	1	longLabel 30-Way Multiz Alignment & Conservation\
parent cons30way\
shortLabel Basewise Conservation (phyloP)\
track cons30wayViewphyloP\
view phyloP\
viewLimits -3.7:4.0\
viewLimitsMax -10.12:5.04\
visibility full\

wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep1	BAT 24wk Al 1	bam	Brown Adipose Tissue Adult 24 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	1	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Brown Adipose Tissue Adult 24 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel BAT 24wk Al 1\
subGroups view=Alignments age=ADULT24WKS cellType=BAT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep1\
type bam\

wgEncodeLicrHistoneBcellcd43nH3k27me3MAdlt8wC57bl6StdPk	BCD43- H3K27m3	broadPeak	B-cell (CD43-) 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	1	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BCD43- H3K27m3\
subGroups view=Peaks age=A1DLT8W factor=H3K27ME3 cellType=B0CELLCD43N control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBcellcd43nH3k27me3MAdlt8wC57bl6StdPk\
type broadPeak\

wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdPk	BM 8w CTCF	broadPeak	Bone Marrow Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	1	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Bone Marrow Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel BM 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xPkRep1	C2 CEBPB 60h 1	narrowPeak	C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	1	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 CEBPB 60h 1\
subGroups view=Peaks factor=CEBPB cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xPkRep1\
type narrowPeak\

wgEncodeCaltechHistC2c12Ab2621FCntrl50bPcr1xPkRep1	C2 H3K79me3 1	narrowPeak	C2C12 H3K79me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	1	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K79me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks off\
shortLabel C2 H3K79me3 1\
subGroups view=Peaks factor=AB2621 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12Ab2621FCntrl50bPcr1xPkRep1\
type narrowPeak\

wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep1	CH12 Aln 1	bam	CH12 RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale	1	1	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale\
origAssembly mm9\
parent wgEncodeSydhRnaSeqViewAlignments\
shortLabel CH12 Aln 1\
subGroups view=Alignments cellType=CH12 readType=R2X101D rnaExtract=RIBOZEROG treatment=NONE rep=rep1\
track wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep1\
type bam\

wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabPk	CH12 BHLHE40	narrowPeak	CH12 BHLHE40 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	1	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 BHLHE40 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 BHLHE40\
subGroups view=Peaks factor=BHLHE40c cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabPk\
type narrowPeak\

wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputPk	CH12 CTCF	broadPeak	CH12 CTCF TFBS ChIP-seq Peaks from ENCODE/PSU	3	1	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 CTCF TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel CH12 CTCF\
subGroups view=Peaks age=IMMORTAL factor=CTCF cellType=CH12 control=INPUT treatment=aNONE rep=repP sex=F strain=s2A4B\
track wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputPk\
type broadPeak\

wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputPk	CH12 H3K4m1	broadPeak	CH12 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	1	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel CH12 H3K4m1\
subGroups view=Peaks age=IMMORTAL factor=H3K04ME1 cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputPk\
type broadPeak\

wgEncodeSydhHistCh12H3k4me3IggyalePk	CH12 H3K4m3 Y	narrowPeak	CH12 H3K4me3 IgG-Yale Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	1	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K4me3 IgG-Yale Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks\
shortLabel CH12 H3K4m3 Y\
subGroups view=Peaks factor=H3K04ME3 cellType=CH12 control=IGGYale treatment=zNONE\
track wgEncodeSydhHistCh12H3k4me3IggyalePk\
type narrowPeak\

wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41SigRep1	CH12 S 1	bigWig 1.000000 28931.000000	CH12 1x41 RNA-seq Signal Rep 1 from ENCODE/PSU	2	1	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 1x41 RNA-seq Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal\
shortLabel CH12 S 1\
subGroups view=Signal age=IMMORTAL cellType=CH12 readType=R1X41 sex=F strain=s2A4B treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41SigRep1\
type bigWig 1.000000 28931.000000\

wgEncodeFsuRepliChipCh12FWaveSignalRep1	CH12 Ws 1	bigWig -1.467918 1.317050	CH12 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	1	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip\
shortLabel CH12 Ws 1\
subGroups view=WaveSignal cellType=CH12 sex=F treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipCh12FWaveSignalRep1\
type bigWig -1.467918 1.317050\

cons30way	Conservation	bed 4	30-Way Multiz Alignment & Conservation	2	1	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track shows multiple alignments of 30 vertebrate\
species and measurements of evolutionary conservation using\
two methods (<em>phastCons</em> and <em>phyloP</em>) from the\
<A HREF="http://compgen.cshl.edu/phast/" target=_BLANK>\
PHAST package</A>, for\
all species (vertebrate) and two subsets (Euarchontoglires and placental mammal).\
The multiple alignments were generated using multiz and\
other tools in the UCSC/<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Penn State Bioinformatics</A>\
comparative genomics alignment pipeline.\
Conserved elements identified by phastCons are also displayed in\
this track.\
</P>\
<P>\
The species are divided into three different groups.\
The Euarchontoglires subset (10 species plus mouse),\
the placental mammal subset (19 species plus mouse),\
and all 30 vertebrate species together.\
These three measurements produce the same results in \
regions where only Euarchontoglires appear in the alignment. \
For other regions, the non-Euarchontoglires species can either \
boost the scores (if conserved) or decrease them (if non-conserved).\
The placental mammal conservation helps to identify sequences that are under \
different evolutionary pressures in mammals and non-mammal vertebrates.\
</P>\
<P>\
<UL>\
<LI> Euarchontoglires subset: mouse(mm9), rat(rn4), Guinea Pig(cavPor2),\
Rabbit(oryCun1), Human(hg18), Chimp(panTro2), Orangutan(ponAbe2),\
Rhesus(rheMac2), Marmoset(calJac1), Bushbaby(otoGar1), Tree Shrew(tupBel1)\
<LI> Placental mammal subset: the Euarchontoglires above plus:\
Shrew(sorAra1), Hedgehog(eriEur1), Dog(canFam2), Cat(felCat3),\
Horse(equCab1), Cow(bosTau3), Armadillo(dasNov1), Elephant(loxAfr1),\
Tenrec(echTel1)\
<LI> Vertebrates: the placentals and Euarchontoglires above plus:\
Opossum(monDom4), Platypus(ornAna1), Chicken(galGal3), Lizard(anoCar1),\
Frog(xenTro2), Tetraodon(tetNig1), Fugu(fr2), Stickleback(gasAcu1),\
Medaka(oryLat1), Zebrafish(danRer5)\
</UL>\
</P>\
<P>\
PhastCons (which has been used in previous Conservation tracks) is a hidden\
Markov model-based method that estimates the probability that each\
nucleotide belongs to a conserved element, based on the multiple alignment.\
It considers not just each individual alignment column, but also its\
flanking columns.  By contrast, phyloP separately measures conservation at\
individual columns, ignoring the effects of their neighbors.  As a\
consequence, the phyloP plots have a less smooth appearance than the\
phastCons plots, with more "texture" at individual sites.  The two methods\
have different strengths and weaknesses.  PhastCons is sensitive to "runs"\
of conserved sites, and is therefore effective for picking out conserved\
elements.  PhyloP, on the other hand, is more appropriate for evaluating\
signatures of selection at particular nucleotides or classes of nucleotides\
(e.g., third codon positions, or first positions of miRNA target sites).\
</P>\
<P>\
Another important difference is that phyloP can measure acceleration\
(faster evolution than expected under neutral drift) as well as\
conservation (slower than expected evolution).  In the phyloP plots, sites\
predicted to be conserved are assigned positive scores (and shown in blue),\
while sites predicted to be fast-evolving are assigned negative scores (and\
shown in red).  The absolute values of the scores represent -log p-values\
under a null hypothesis of neutral evolution.  The phastCons scores, by\
contrast, represent probabilities of negative selection and range between 0\
and 1.\
</P>\
<P>\
Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as\
missing data, and both were run with the same parameters for each\
species set (vertebrates, placental mammals, and Euarchontoglires).\
Thus, in regions in which only Euarchontoglires appear in the alignment, all three\
sets of scores will be the same, but in regions in which additional species\
are available, the mammalian and/or vertebrate scores may differ from the\
Euarchontoglires scores.  The alternative\
plots help to identify sequences that are under different evolutionary\
pressures in, say, Euarchontoglires and non-Euarchontoglires, or mammals and non-mammals.\
</P>\
\
<P>\
The multiple alignments were generated using multiz and \
other tools in the UCSC/<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Penn State Bioinformatics</A>\
comparative genomics alignment pipeline.\
The conservation measurements were created using the phastCons package from\
<A HREF="http://siepellab.labsites.cshl.edu/" TARGET=_blank>\
Adam Siepel</A> at Cold Spring Harbor Laboratory. </P>\
<P>\
Details of the alignment parameters are noted in the genomewiki\
<A HREF="http://genomewiki.ucsc.edu/index.php/Mm9_multiple_alignment"\
TARGET=_blank>Mm9 multiple alignment</A> page.\
</P>\
<P>\
The species aligned for this track include the reptile, amphibian, \
bird, and fish clades, as well as marsupial, monotreme (platypus), \
and placental mammals. Compared to the previous 17-vertebrate alignment,\
this track includes 13 new species and 4 species with updated\
sequence assemblies (<B>Table 1</B>). The new species consist of seven \
high-coverage (5-8.5X) assemblies (orangutan, marmoset, horse, platypus, \
lizard, and two teleost fish: stickleback and medaka)\
and six low-coverage (2X) genome assemblies from mammalian species selected for \
sampling by NHGRI (bushbaby, tree shrew, guinea pig, \
hedgehog, common shrew, and cat).\
The cow, chicken, fugu, and zebrafish assemblies in this \
track have been updated from those used in the previous 17-species alignment.\
</P>\
<P>\
UCSC has repeatmasked and aligned the low-coverage genome assemblies, and\
provides the sequence for download; however, we do not construct\
genome browsers for them. Missing sequence in the low-coverage assemblies is\
highlighted in the track display by regions of yellow when zoomed out\
and Ns displayed at base level (see <EM>Gap Annotation</EM>, below). </P>\
<P>\
<BLOCKQUOTE><TABLE BORDER=1 CELLPADDING=4 BORDERCOLOR="#aaaaaa">\
<TR ALIGN=left><TH>Organism</TH><TH>Species</TH><TH>Release date</TH><TH>UCSC version</TH></TR>\
<TR ALIGN=left><TD>Mouse</TD><TD>Mus musculus</TD><TD>\
    Jul 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=mm9"\
    TARGET=_blank>mm9</A></TD></TR>\
<TR ALIGN=left><TD>Armadillo</TD><TD>Dasypus novemcinctus</TD><TD>May 2005</TD>\
    <TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/dasNov1/"\
    TARGET=_blank>dasNov1</A>*</TD></TR>\
<TR ALIGN=left><TD>Bushbaby</TD><TD>Otolemur garnetti</TD><TD>Dec 2006</TD>\
    <TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/otoGar1/"\
    TARGET=_blank>otoGar1</A>*</TD></TR>\
<TR ALIGN=left><TD>Cat</TD><TD>Felis catus</TD><TD>\
    Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=felCat3"\
    TARGET=_blank>felCat3</A></TD></TR>\
<TR ALIGN=left><TD>Chicken</TD><TD>Gallus gallus</TD><TD>\
    May 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=galGal3"\
    TARGET=_blank>galGal3</A></TD></TR>\
<TR ALIGN=left><TD>Chimpanzee</TD><TD>Pan troglodytes</TD><TD>\
    Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=panTro2"\
    TARGET=_blank>panTro2</A></TD></TR>\
<TR ALIGN=left><TD>Cow</TD><TD>Bos taurus</TD><TD>\
    Aug 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=bosTau3"\
    TARGET=_blank>bosTau3</A></TD></TR>\
<TR ALIGN=left><TD>Dog</TD><TD>Canis familiaris</TD><TD>\
    May 2005</TD><TD> <A HREF="../cgi-bin/hgGateway?db=canFam2"\
    TARGET=_blank>canFam2</A></TD></TR>\
<TR ALIGN=left><TD>Elephant</TD><TD>Loxodonta africana</TD><TD>May 2005</TD>\
    <TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/loxAfr1/"\
    TARGET=_blank>loxAfr1</A>*</TD></TR>\
<TR ALIGN=left><TD>Frog</TD><TD>Xenopus tropicalis</TD><TD>\
    Aug 2005</TD><TD> <A HREF="../cgi-bin/hgGateway?db=xenTro2"\
    TARGET=_blank>xenTro2</A></TD></TR>\
<TR ALIGN=left><TD>Fugu</TD><TD>Takifugu rubripes</TD><TD>\
    Oct 2004</TD><TD> <A HREF="../cgi-bin/hgGateway?db=fr2"\
    TARGET=_blank>fr2</A></TD></TR>\
<TR ALIGN=left><TD>Guinea pig</TD><TD>Cavia porcellus</TD><TD>Oct 2005</TD>\
    <TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/cavPor2/"\
    TARGET=_blank>cavPor2</A>*</TD></TR>\
<TR ALIGN=left><TD>Hedgehog</TD><TD>Erinaceus europaeus</TD><TD>June 2006</TD>\
    <TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/eriEur1/"\
    TARGET=_blank>eriEur1</A>*</TD></TR>\
<TR ALIGN=left><TD>Horse</TD><TD>Equus caballus</TD><TD>\
    Jan 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=equCab1"\
    TARGET=_blank>equCab1</A></TD></TR>\
<TR ALIGN=left><TD>Human</TD><TD>Homo sapiens</TD><TD>\
    Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=hg18"\
    TARGET=_blank>hg18</A></TD></TR>\
<TR ALIGN=left><TD>Lizard</TD><TD>Anolis carolinensis</TD><TD>\
    Feb 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=anoCar1"\
    TARGET=_blank>anoCar1</A></TD></TR>\
<TR ALIGN=left><TD>Marmoset</TD><TD>Callithrix jacchus</TD><TD>June 2007</TD>\
    <TD><A HREF="../cgi-bin/hgGateway?db=calJac1"\
    TARGET=_blank>calJac1</A></TD></TR>\
<TR ALIGN=left><TD>Medaka</TD><TD>Oryzias latipes</TD><TD>\
    Apr 2006</TD><TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/oryLat1/"\
    TARGET=_blank>oryLat1</A>*</TD></TR>\
<TR ALIGN=left><TD>Opossum</TD><TD>Monodelphis domestica</TD><TD>\
    Jan 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=monDom4"\
    TARGET=_blank>monDom4</A></TD></TR>\
<TR ALIGN=left><TD>Orangutan</TD><TD>Pongo pygmaeus abelii</TD><TD>\
    July 2007</TD><TD><A HREF="../cgi-bin/hgGateway?db=ponAbe2"\
    TARGET=_blank>ponAbe2</A></TD></TR>\
<TR ALIGN=left><TD>Platypus</TD><TD>Ornithorhychus anatinus</TD><TD>\
    Mar 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=ornAna1"\
    TARGET=_blank>ornAna1</A></TD></TR>\
<TR ALIGN=left><TD>Rabbit</TD><TD>Oryctolagus cuniculus</TD><TD>May 2005</TD>\
    <TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/oryCun1/"\
    TARGET=_blank>oryCun1</A>*</TD></TR>\
<TR ALIGN=left><TD>Rat</TD><TD>Rattus norvegicus</TD><TD>\
    Nov 2004</TD><TD> <A HREF="../cgi-bin/hgGateway?db=rn4"\
    TARGET=_blank>rn4</A></TD></TR>\
<TR ALIGN=left><TD>Rhesus</TD><TD>Macaca mulatta</TD><TD>\
    Jan 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=rheMac2"\
    TARGET=_blank>rheMac2</A></TD></TR>\
<TR ALIGN=left><TD>Shrew</TD><TD>Sorex araneus</TD><TD>June 2006</TD>\
    <TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/sorAra1/"\
    TARGET=_blank>sorAra1</A>*</TD></TR>\
<TR ALIGN=left><TD>Stickleback</TD><TD>Gasterosteus aculeatus</TD><TD>\
    Feb 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=gasAcu1"\
    TARGET=_blank>gasAcu1</A></TD></TR>\
<TR ALIGN=left><TD>Tenrec</TD><TD>Echinops telfairi</TD><TD>July 2005</TD>\
    <TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/echTel1/"\
    TARGET=_blank>echTel1</A>*</TD></TR>\
<TR ALIGN=left><TD>Tetraodon</TD><TD>Tetraodon nigroviridis</TD><TD>\
    Feb 2004</TD><TD> <A HREF="../cgi-bin/hgGateway?db=tetNig1"\
    TARGET=_blank>tetNig1</A></TD></TR>\
<TR ALIGN=left><TD>Tree shrew</TD><TD>Tupaia belangeri</TD><TD>Dec 2006</TD>\
    <TD><A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/tupBel1/"\
    TARGET=_blank>tupBel1</A>*</TD></TR>\
<TR ALIGN=left><TD>Zebrafish</TD><TD>Danio rerio</TD><TD>\
    July 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=danRer5"\
    TARGET=_blank>danRer5</A></TD></TR>\
</TABLE><BR>\
<B>Table 1.</B> <EM>Genome assemblies included in the 30-way Conservation \
track.</EM>\
<BR>* Data download only, browser not available.\
</BLOCKQUOTE></P>\
\
Downloads for data in this track are available:\
<UL>\
<LI>\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/multiz30way/">Multiz alignments</A> (MAF format), and phylogenetic trees\
<LI>\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/phyloP30way/">PhyloP conservation</A> (WIG format)\
<LI>\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/phastCons30way/">PhastCons conservation</A> (WIG format)\
</UL>\
\
<H2>Display Conventions and Configuration</H2>\
<P>\
In full and pack display modes, conservation scores are displayed as\
<EM>wiggle tracks</EM> (histograms) in which the height reflects the \
size of the score. \
The conservation wiggles can be configured in a variety of ways to \
highlight different aspects of the displayed information. \
Click the <A HREF="../goldenPath/help/hgWiggleTrackHelp.html" \
TARGET=_blank>Graph configuration help</A> link for an explanation \
of the configuration options.</P>\
<P>\
Pairwise alignments of each species to the mouse genome are \
displayed below the conservation histogram as a grayscale density plot (in \
pack mode) or as a wiggle (in full mode) that indicates alignment quality.\
In dense display mode, conservation is shown in grayscale using\
darker values to indicate higher levels of overall conservation \
as scored by phastCons. </P>\
<P>\
Checkboxes on the track configuration page allow selection of the\
species to include in the pairwise display.  \
Configuration buttons are available to select all of the species (<EM>Set \
all</EM>), deselect all of the species (<EM>Clear all</EM>), or \
use the default settings (<EM>Set defaults</EM>).\
By default, the following 8 species are included in the pairwise display:\
rat, human, orangutan, dog, horse, opossum, chicken, and stickleback.\
Note that excluding species from the pairwise display does not alter the\
the conservation score display.</P>\
<P>\
To view detailed information about the alignments at a specific\
position, zoom the display in to 30,000 or fewer bases, then click on\
the alignment.</P>\
\
<H3>Gap Annotation</H3>\
<P>\
The <EM>Display chains between alignments</EM> configuration option \
enables display of gaps between alignment blocks in the pairwise alignments in \
a manner similar to the Chain track display.  The following\
conventions are used:\
<UL>\
<LI><B>Single line:</B> No bases in the aligned species. Possibly due to a\
lineage-specific insertion between the aligned blocks in the mouse genome\
or a lineage-specific deletion between the aligned blocks in the aligning\
species.\
<LI><B>Double line:</B> Aligning species has one or more unalignable bases in\
the gap region. Possibly due to excessive evolutionary distance between \
species or independent indels in the region between the aligned blocks in both\
species. \
<LI><B>Pale yellow coloring:</B> Aligning species has Ns in the gap region.\
Reflects uncertainty in the relationship between the DNA of both species, due\
to lack of sequence in relevant portions of the aligning species. \
</UL></P>\
\
<H3>Genomic Breaks</H3>\
<P>\
Discontinuities in the genomic context (chromosome, scaffold or region) of the\
aligned DNA in the aligning species are shown as follows: \
<UL>\
<LI>\
<B>Vertical blue bar:</B> Represents a discontinuity that persists indefinitely\
on either side, <em>e.g.</em> a large region of DNA on either side of the bar\
comes from a different chromosome in the aligned species due to a large scale\
rearrangement. \
<LI>\
<B>Green square brackets:</B> Enclose shorter alignments consisting of DNA from\
one genomic context in the aligned species nested inside a larger chain of\
alignments from a different genomic context. The alignment within the\
brackets may represent a short misalignment, a lineage-specific insertion of a\
transposon in the mouse genome that aligns to a paralogous copy somewhere\
else in the aligned species, or other similar occurrence.\
</UL></P>\
\
<H3>Base Level</H3>\
<P>\
When zoomed-in to the base-level display, the track shows the base \
composition of each alignment. \
The numbers and symbols on the Gaps\
line indicate the lengths of gaps in the mouse sequence at those \
alignment positions relative to the longest non-mouse sequence. \
If there is sufficient space in the display, the size of the gap is shown. \
If the space is insufficient and the gap size is a multiple of 3, a \
&quot;*&quot; is displayed; other gap sizes are indicated by &quot;+&quot;.</P>\
<P>\
Codon translation is available in base-level display mode if the\
displayed region is identified as a coding segment. To display this annotation,\
select the species for translation from the pull-down menu in the Codon\
Translation configuration section at the top of the page. Then, select one of\
the following modes:\
<UL>\
<LI> \
<B>No codon translation:</B> The gene annotation is not used; the bases are\
displayed without translation. \
<LI>\
<B>Use default species reading frames for translation:</B> The annotations from the genome\
displayed \
in the <EM>Default species to establish reading frame</EM> pull-down menu are used to\
translate all the aligned species present in the alignment. \
<LI>\
<B>Use reading frames for species if available, otherwise no translation:</B> Codon\
translation is performed only for those species where the region is\
annotated as protein coding.\
<LI><B>Use reading frames for species if available, otherwise use default species:</B>\
Codon translation is done on those species that are annotated as being protein\
coding over the aligned region using species-specific annotation; the remaining\
species are translated using the default species annotation. \
</UL></P>\
<P>\
Codon translation uses the following gene tracks as the basis for\
translation, depending on the species chosen (<B>Table 2</B>).  \
Species listed in the row labeled &quot;None&quot; do not have \
species-specific reading frames for gene translation.\
\
<BLOCKQUOTE><TABLE BORDER=1 CELLPADDING=4 BORDERCOLOR="#aaaaaa">\
<TR ALIGN=left><TD><B>Gene Track</B></TD><TD><B>Species</B></TD></TR>\
<TR ALIGN=left><TD>Known Genes</TD><TD>human, mouse</TD></TR>\
<TR ALIGN=left><TD>Ensembl Genes</TD><TD>rat, rhesus, chimp, dog, opossum, platypus,\
zebrafish, fugu, stickleback, medaka</TD></TR>\
<TR ALIGN=left><TD>RefSeq Genes</TD><TD>cow, frog</TD></TR>\
<TR ALIGN=left><TD>mRNAs</TD><TD>orangutan, elephant, rabbit, cat, horse,\
chicken, lizard, armadillo, tetraodon</TD></TR>\
<TR ALIGN=left><TD>None</TD><TD>marmoset, bushbaby, tree shrew, guinea pig,\
shrew, hedgehog, tenrec</TD></TR>\
</TABLE>\
<B>Table 2.</B> <EM>Gene tracks used for codon translation.</EM>\
</BLOCKQUOTE></P>\
\
<H2>Methods</H2>\
<P> \
Pairwise alignments with the mouse genome were generated for \
each species using lastz from repeat-masked genomic sequence. \
Pairwise alignments were then linked into chains using a dynamic programming\
algorithm that finds maximally scoring chains of gapless subsections\
of the alignments organized in a kd-tree.\
The scoring matrix and parameters for pairwise alignment and chaining\
were tuned for each species based on phylogenetic distance from the reference.\
High-scoring chains were then placed along the genome, with\
gaps filled by lower-scoring chains, to produce an alignment net.\
For more information about the chaining and netting process and \
parameters for each species, see the description pages for the Chain and Net \
tracks.</P>\
<P>\
An additional filtering step was introduced in the generation of the 30-way\
conservation track to reduce the number of paralogs and pseudogenes from the \
high-quality assemblies and the suspect alignments from the low-quality \
assemblies:\
the pairwise alignments of high-quality mammalian \
sequences (placental and marsupial) were filtered based on synteny; \
those for 2X mammalian genomes were filtered to retain only \
alignments of best quality in both the target and query (&quot;reciprocal \
best&quot;).</P>\
<P>\
The resulting best-in-genome pairwise alignments\
were progressively aligned using multiz/autoMZ, \
following the tree topology diagrammed above, to produce multiple alignments.\
The multiple alignments were post-processed to\
add annotations indicating alignment gaps, genomic breaks,\
and base quality of the component sequences.\
The annotated multiple alignments, in MAF format, are available for\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/multiz30way"\
TARGET=_blank>bulk download</A>.\
An alignment summary table containing an entry for each\
alignment block in each species was generated to improve\
track display performance at large scales.\
Framing tables were constructed to enable\
visualization of codons in the multiple alignment display.</P>\
\
<h3> Phylogenetic Tree Model</h3>\
<P>\
Both <em>phastCons</em> and <em>phyloP</em> are phylogenetic methods that\
rely on a tree model containing the tree topology,\
branch lengths representing evolutionary distance at neutrally\
evolving sites, the background distribution of nucleotides, and a substitution\
rate matrix.  The \
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/phastCons30way/vertebrate.mod"\
TARGET=_blank>vertebrate tree model</A> for this track was\
generated using the <em>phyloFit</em> program from the PHAST package  \
(REV model, EM algorithm, medium precision) using multiple alignments of \
4-fold degenerate sites extracted from the 30-way alignment\
(msa_view).  The 4d sites were derived from the \
<A HREF="https://genome.crg.es/gencode/" TARGET=_blank>Oct 2005 Gencode \
Reference Gene set</A>,\
which was filtered to select single-coverage long transcripts. The\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/phastCons30way/placental.mod" \
TARGET=_blank>placental mammal tree model</A> and the\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/phastCons30way/euarchontoglires.mod" \
TARGET=_blank>Euarchontoglires tree model</A> were extracted from the vertebrate model.\
The phastCons parameters were\
tuned to produce 5% conserved elements in the genome for the vertebrate\
conservation measurement.  This parameter set (expected-length=45, \
target-coverage=.3, rho=.31) was then used to generate the placental\
mammal and Euarchontoglires conservation scoring.</P>\
<P>\
The phastCons program computes conservation scores based on a phylo-HMM, a\
type of probabilistic model that describes both the process of DNA\
substitution at each site in a genome and the way this process changes from\
one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and\
Haussler 2005).  PhastCons uses a two-state phylo-HMM, with a state for\
conserved regions and a state for non-conserved regions.  The value plotted\
at each site is the posterior probability that the corresponding alignment\
column was "generated" by the conserved state of the phylo-HMM.  These\
scores reflect the phylogeny (including branch lengths) of the species in\
question, a continuous-time Markov model of the nucleotide substitution\
process, and a tendency for conservation levels to be autocorrelated along\
the genome (i.e., to be similar at adjacent sites).  The general reversible\
(REV) substitution model was used.  Unlike many conservation-scoring programs, \
note that phastCons does not rely on a sliding window\
of fixed size; therefore, short highly-conserved regions and long moderately\
conserved regions can both obtain high scores.  More information about\
phastCons can be found in Siepel <EM>et al</EM>. 2005.</P> \
<P> \
PhastCons currently treats alignment gaps as missing data, which\
sometimes has the effect of producing undesirably high conservation scores\
in gappy regions of the alignment.  We are looking at several possible ways\
of improving the handling of alignment gaps.</P>\
\
<h3> PhyloP Conservation </h3>\
<P>\
The phyloP program supports several different methods for computing\
p-values of conservation or acceleration, for individual nucleotides or\
larger elements (<a href="http://compgen.cshl.edu/phast/" target="_blank">\
http://compgen.cshl.edu/phast/</a>).  Here it was used\
to produce separate scores at each base (--wig-scores option), considering\
all branches of the phylogeny rather than a particular subtree or lineage\
(i.e., the --subtree option was not used).  The scores were computed by\
performing a likelihood ratio test at each alignment column (--method LRT),\
and scores for both conservation and acceleration were produced (--mode\
CONACC).\
</P>\
<h3> Conserved Elements </h3>\
<P>\
The conserved elements were predicted by running phastCons with the\
--viterbi option.  The predicted elements are segments of the alignment\
that are likely to have been "generated" by the conserved state of the\
phylo-HMM. Each element is assigned a log-odds score equal to its log\
probability under the conserved model minus its log probability under the\
non-conserved model. The "score" field associated with this track contains\
transformed log-odds scores, taking values between 0 and 1000. (The scores\
are transformed using a monotonic function of the form a * log(x) + b.) The\
raw log odds scores are retained in the "name" field and can be seen on the\
details page or in the browser when the track's display mode is set to\
"pack" or "full".\
</P>\
\
<H2>Credits</H2>\
<P> This track was created using the following programs:\
<UL>\
<LI> Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz and Webb \
Miller of the <A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Penn State Bioinformatics Group</A>\
<LI> Chaining and Netting:  axtChain, chainNet by Jim Kent at UCSC\
<LI> Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view\
and other programs in PHAST by \
<A HREF="http://siepellab.labsites.cshl.edu/"\
TARGET=_blank>Adam Siepel</A> at Cold Spring Harbor Laboratory (original development\
done at the Haussler lab at UCSC).\
<LI> MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows\
by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC\
<LI> Tree image generator: phyloPng by Galt Barber, UCSC\
<LI> Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle \
display), and Brian Raney (gap annotation and codon framing) at UCSC\
</UL>\
</P>\
<P>The phylogenetic tree is based on Murphy <EM>et al</EM>. (2001) and general \
consensus in the vertebrate phylogeny community as of March 2007.\
</P>\
\
<H2>References</H2>\
\
<H3>Phylo-HMMs, phastCons, and phyloP:</H3>\
<p>\
Felsenstein J, Churchill GA.\
<a href="https://academic.oup.com/mbe/article/13/1/93/1055515"\
target="_blank">A Hidden Markov Model approach to\
variation among sites in rate of evolution</a>.\
<em>Mol Biol Evol</em>. 1996 Jan;13(1):93-104.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8583911" target="_blank">8583911</a>\
</p>\
\
<p>\
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K,\
Clawson H, Spieth J, Hillier LW, Richards S, <em>et al.</em>\
<a href="https://genome.cshlp.org/content/15/8/1034"\
target="_blank">Evolutionarily conserved elements in vertebrate, insect, worm,\
and yeast genomes</a>.\
<em>Genome Res</em>. 2005 Aug;15(8):1034-50.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16024819" target="_blank">16024819</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182216/" target="_blank">PMC1182216</a>\
</p>\
\
<p>\
Siepel A, Haussler D.\
<a href="http://compgen.cshl.edu/~acs/phylohmm.pdf"\
target="_blank">Phylogenetic Hidden Markov Models</a>.\
In: Nielsen R, editor. Statistical Methods in Molecular Evolution.\
New York: Springer; 2005. pp. 325-351.\
</p>\
\
<p>\
Yang Z.\
<a href="https://www.genetics.org/content/139/2/993"\
target="_blank">A space-time process model for the evolution of DNA\
sequences</a>.\
<em>Genetics</em>. 1995 Feb;139(2):993-1005.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/7713447" target="_blank">7713447</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1206396/" target="_blank">PMC1206396</a>\
</p>\
\
<H3>Chain/Net:</H3>\
<p>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<a href="https://www.pnas.org/content/100/20/11484"\
target="_blank">Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<H3>Multiz:</H3>\
<p>\
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM,\
Baertsch R, Rosenbloom K, Clawson H, Green ED, <em>et al.</em>\
<a href="https://genome.cshlp.org/content/14/4/708.abstract"\
target="_blank">Aligning multiple genomic sequences with the threaded blockset aligner</a>.\
<em>Genome Res</em>. 2004 Apr;14(4):708-15.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15060014" target="_blank">15060014</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC383317/" target="_blank">PMC383317</a>\
</p>\
\
<H3>Lastz (formerly Blastz):</H3>\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<a href="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
target="_blank">Scoring pairwise genomic sequence alignments</a>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<p>\
Harris RS.\
<a href="http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf"\
target="_blank">Improved pairwise alignment of genomic DNA</a>.\
<em>Ph.D. Thesis</em>. Pennsylvania State University, USA. 2007.\
</p>\
\
<p>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<a href="https://genome.cshlp.org/content/13/1/103.abstract"\
target="_blank">Human-mouse alignments with BLASTZ</a>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
\
<H3>Phylogenetic Tree:</H3>\
<p>\
Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E,\
Ryder OA, Stanhope MJ, de Jong WW, Springer MS.\
<a href="https://science.sciencemag.org/content/294/5550/2348"\
target="_blank">Resolution of the early placental mammal radiation using Bayesian phylogenetics</a>.\
<em>Science</em>. 2001 Dec 14;294(5550):2348-51.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11743200" target="_blank">11743200</a>\
</p>\
	compGeno	1	compositeTrack on\
dimensions dimensionX=clade\
dragAndDrop subTracks\
group compGeno\
longLabel 30-Way Multiz Alignment & Conservation\
priority 1\
shortLabel Conservation\
subGroup1 view Views align=Multiz_Alignments phyloP=Basewise_Conservation_(phyloP) phastcons=Element_Conservation_(phastCons) elements=Conserved_Elements\
subGroup2 clade Clade glires=Euarchontoglires mammal=Mammal vert=Vertebrate\
track cons30way\
type bed 4\
visibility full\

cons30wayViewelements	Conserved Elements	bed 4	30-Way Multiz Alignment & Conservation	0	1	0	0	0	127	127	127	0	0	0				compGeno	1	longLabel 30-Way Multiz Alignment & Conservation\
parent cons30way\
shortLabel Conserved Elements\
track cons30wayViewelements\
view elements\
visibility hide\

cpgIslandExt	CpG Islands	bed 4 +	CpG Islands (Islands < 300 Bases are Light Green)	3	1	0	100	0	128	228	128	0	0	0			<h2>Description</h2>\
\
<p>CpG islands are associated with genes, particularly housekeeping\
genes, in vertebrates.  CpG islands are typically common near\
transcription start sites and may be associated with promoter\
regions.  Normally a C (cytosine) base followed immediately by a \
G (guanine) base (a CpG) is rare in\
vertebrate DNA because the Cs in such an arrangement tend to be\
methylated.  This methylation helps distinguish the newly synthesized\
DNA strand from the parent strand, which aids in the final stages of\
DNA proofreading after duplication.  However, over evolutionary time,\
methylated Cs tend to turn into Ts because of spontaneous\
deamination.  The result is that CpGs are relatively rare unless\
there is selective pressure to keep them or a region is not methylated\
for some other reason, perhaps having to do with the regulation of gene\
expression.  CpG islands are regions where CpGs are present at\
significantly higher levels than is typical for the genome as a whole.</p>\
\
<p>\
The unmasked version of the track displays potential CpG islands\
that exist in repeat regions and would otherwise not be visible\
in the repeat masked version.\
</p>\
\
<p>\
By default, only the masked version of the track is displayed.  To view the\
unmasked version, change the visibility settings in the track controls at\
the top of this page.\
</p>\
\
<h2>Methods</h2>\
\
<p>CpG islands were predicted by searching the sequence one base at a\
time, scoring each dinucleotide (+17 for CG and -1 for others) and\
identifying maximally scoring segments.  Each segment was then\
evaluated for the following criteria:\
\
<ul>\
\	<li>GC content of 50% or greater</li>\
\	<li>length greater than 200 bp</li>\
\	<li>ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the \
\	basis of the number of Gs and Cs in the segment</li>\
</ul>\
</p>\
<p>\
The entire genome sequence, masking areas included, was\
used for the construction of the  track <em>Unmasked CpG</em>.\
The track <em>CpG Islands</em> is constructed on the sequence after\
all masked sequence is removed.\
</p>\
\
<p>The CpG count is the number of CG dinucleotides in the island.  \
The Percentage CpG is the ratio of CpG nucleotide bases\
(twice the CpG count) to the length.  The ratio of observed to expected \
CpG is calculated according to the formula (cited in \
Gardiner-Garden <em>et al</em>. (1987)):\
\
<pre>    Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)</pre>\
\
where N = length of sequence.</p>\
<p>\
The calculation of the track data is performed by the following command sequence:\
<pre>\
twoBitToFa <em>assembly.2bit</em> stdout | maskOutFa stdin hard stdout \\\
  | cpg_lh /dev/stdin 2&gt; cpg_lh.err \\\
    |  awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2;  printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \\\
     | sort -k1,1 -k2,2n &gt; cpgIsland.bed\
</pre>\
The <em>unmasked</em> track data is constructed from\
<em>twoBitToFa -noMask</em> output for the <em>twoBitToFa</em> command.\
</p>\
\
<h2>Data access</h2>\
<p>\
CpG islands and its associated tables can be explored interactively using the\
<a href="../goldenPath/help/api.html" target="_blank">REST API</a>, the\
<a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> or the\
<a href="/cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>.\
All the tables can also be queried directly from our public MySQL\
servers, with more information available on our\
<a target="_blank" href="/goldenPath/help/mysql.html">help page</a> as well as on\
<a target="_blank" href="http://genome.ucsc.edu/blog/tag/mysql/">our blog</a>.</p>\
<p>\
The source for the <em>cpg_lh</em> program can be obtained from\
<a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/tree/master/src/utils/cpgIslandExt/" target=_blank>src/utils/cpgIslandExt/</a>.\
The <em>cpg_lh</em> program binary can be obtained from: <a href="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh" download="cpg_lh">http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh</a> (choose "save file")\
</p>\
\
<h2>Credits</h2>\
\
<p>This track was generated using a modification of a program developed by G. Miklem and L. Hillier \
(unpublished).</p>\
\
<h2>References</h2>\
\
<p>\
Gardiner-Garden M, Frommer M.\
<a href="https://www.sciencedirect.com/science/article/pii/0022283687906899" target="_blank">\
CpG islands in vertebrate genomes</a>.\
<em>J Mol Biol</em>. 1987 Jul 20;196(2):261-82.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/3656447" target="_blank">3656447</a>\
</p>\
	regulation	1	html cpgIslandSuper\
longLabel CpG Islands (Islands < 300 Bases are Light Green)\
parent cpgIslandSuper pack\
priority 1\
shortLabel CpG Islands\
track cpgIslandExt\

wgEncodeCrgMapabilityAlign36mer	CRG Align 36	bigWig 0.00 1.00	Alignability of 36mers by GEM from ENCODE/CRG(Guigo)	0	1	120	0	0	187	127	127	0	0	0				map	0	color 120,0,0\
longLabel Alignability of 36mers by GEM from ENCODE/CRG(Guigo)\
parent wgEncodeMapability\
priority 1\
shortLabel CRG Align 36\
subGroups win=w036 lab=CRG\
track wgEncodeCrgMapabilityAlign36mer\

cons30wayViewphastcons	Element Conservation (phastCons)	bed 4	30-Way Multiz Alignment & Conservation	0	1	0	0	0	127	127	127	0	0	0				compGeno	1	longLabel 30-Way Multiz Alignment & Conservation\
parent cons30way\
shortLabel Element Conservation (phastCons)\
track cons30wayViewphastcons\
view phastcons\
visibility hide\

phyloP30wayEuarch	Euarch Cons	wig -7.49 1.13	Euarchontoglires Basewise Conservation by PhyloP	2	1	10	10	70	70	10	10	0	0	0				compGeno	0	altColor 70,10,10\
autoScale off\
color 10,10,70\
configurable on\
longLabel Euarchontoglires Basewise Conservation by PhyloP\
maxHeightPixels 100:50:11\
noInherit on\
parent cons30wayViewphyloP off\
priority 1\
shortLabel Euarch Cons\
spanList 1\
subGroups view=phyloP clade=glires\
track phyloP30wayEuarch\
type wig -7.49 1.13\
viewLimits -3:1.2\
windowingFunction mean\

wgEncodePsuDnaseG1eS129ME0PkRep1	G1E 1	narrowPeak	G1E DNaseI HS Peaks Rep 1 from ENCODE/PSU	3	1	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E DNaseI HS Peaks Rep 1 from ENCODE/PSU\
parent wgEncodePsuDnaseViewPeaks\
shortLabel G1E 1\
subGroups view=Peaks age=E0 cellType=G1E sex=M strain=S129 treatment=aNONE rep=rep1\
track wgEncodePsuDnaseG1eS129ME0PkRep1\
type narrowPeak\

pubsBlatPsl	Indiv. Seq. Matches	psl	Individual Sequence Matches of One Selected Article from Sequences Track	0	1	0	115	70	127	185	162	0	0	0				pub	1	color 0,115,70\
configurable off\
configureByPopup off\
longLabel Individual Sequence Matches of One Selected Article from Sequences Track\
parent pubs off\
priority 1\
shortLabel Indiv. Seq. Matches\
track pubsBlatPsl\
type psl\
visibility hide\

cons30wayViewalign	Multiz Alignments	bed 4	30-Way Multiz Alignment & Conservation	3	1	0	0	0	127	127	127	0	0	0				compGeno	1	longLabel 30-Way Multiz Alignment & Conservation\
parent cons30way\
shortLabel Multiz Alignments\
track cons30wayViewalign\
view align\
viewUi on\
visibility pack\

numtS	NumtS	bed 6 .	Mouse NumtS	0	1	0	60	120	127	157	187	1	0	0			<h2>Description and display conventions</h2>\
\
<p> <b>NumtS</b> (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear\
genomic sequences. The most credited hypothesis concerning their generation suggests that in presence\
of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach\
the nucleus and insert into chromosomes during break repair; although NumtS can also derive from\
duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing\
and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group\
chaired by M. Attimonelli (University of Bari, Italy) has produced the RMmsNumtS (Reference Mus musculus\
NumtS) compilation annotating 148 Mouse assembled NumtS. To allow the scientific community to access \
the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the\
group has designed the Mouse NumtS tracks described below. </p>\
\
<p>The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs)\
obtained by aligning the mitochondrial reference genome (NC_005089) with the mm9 assembly of the\
mouse genome.</p> \
\
<ol> \
\	<li><b>"NumtS (Nuclear mitochondrial Sequences)" Track</b> \
\	<p> The "NumtS\
mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear\
genome. The shading of the items reflect the similarity returned by BlastN, and the direction of\
the arrows is concordant with the strand of the alignment. For every item, a link pointing to the\
mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. </p>\
\	</li>\
\
\	<li><b>"NumtS assembled" Track</b> \
\	<p> The "NumtS assembled" track shows items obtained by\
assembling HSPs annotated in the "NumtS" track fulfilling the following conditions:</p>\
\
\	\	<ul>\
\	\	\	<li>The orientation of their alignments must be concordant.</li> \
\	\	\	<li>The distance between them must be less than 2 kb, on the mitochondrial genome as \
\	\	\	well as on the nuclear genome.</li> \
\	\	</ul> \
\	\	\
\	<p>Exceptions for the second condition arise when a long repetitive element is present between\
\	 two HSPs.</p></li>\
\
\	<li><b>"NumtS on mitochondrion" Track</b>\
\	<p>The "NumtS on mitochondrion" track shows the mapping\
of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned\
by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every\
item, a link pointing to the nuclear mapping is provided.</p></li>\
\
\	<li><b>"Mouse NumtS on mitochondrion SNP" Track</b> \
\	<p>The "Mouse NumtS SNP" shows the mapping of\
the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison\
with the mm9 assembly. No shading is here provided. For every item, a link pointing to the nuclear\
mapping is provided.</p></li>\
</ol>\
\
<h2>Methods</h2> \
\
<p>NumtS mappings were obtained by running Blast2seq (program: BlastN) between\
each chromosome of the Mouse Genome (mm9 assembly) and the mouse mitochondrial reference sequence (AC:\
NC_005089), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with\
spreadsheet interpolation and manual inspection. BED format is used for the first three annotation\
tracks, while for the last one the SAM/BAM format is preferred.</p>\
\
<h2>Credits</h2>\
\
<p>These data were provided by Francesco Maria Calabrese, Domenico Simone and\
Marcella Attimonelli from the Department of Biochemistry and Molecular Biology "Ernesto \
Quagliariello" (University of Bari, Italy). Manual inspection and format details are carried out \
by Francesco Maria Calabrese, Domenico Simone and Luana Raddi.</p>\
\
<h2>References</h2>\
\
<p>\
Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M.\
<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-267" target="_blank">\
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human\
NumtS</a>.\
<em>BMC Genomics</em>. 2008 Jun 3;9:267.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18522722" target="_blank">18522722</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447851" target="_blank">PMC2447851</a>\
</p>\
\
<p>\
Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M.\
<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-517" target="_blank">\
The reference human nuclear mitochondrial sequences compilation validated and implemented on the\
UCSC genome browser</a>.\
<em>BMC Genomics</em>. 2011 Oct 20;12:517.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22013967" target="_blank">22013967</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228558" target="_blank">PMC3228558</a>\
</p>\
\
\
	varRep	1	color 0,60,120\
html numtSeqMm9\
longLabel Mouse NumtS\
parent numtSeq\
priority 1\
shortLabel NumtS\
track numtS\
type bed 6 .\
useScore 1\

polyASeqSitesBrainFwd	PolyA-Seq Brain	bigWig 0.840000 79444.007812	Poly(A)-tail sequencing of Brain from Merck (Fwd strand)	2	1	153	51	51	204	153	153	0	0	0				rna	0	color 153,51,51\
longLabel Poly(A)-tail sequencing of Brain from Merck (Fwd strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Brain\
subGroups view=Signal tissType=Brain strand=fwd\
track polyASeqSitesBrainFwd\
type bigWig 0.840000 79444.007812\

pubs	Publications	bed 4	Publications: Sequences in Scientific Articles	1	1	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>This track is based on text-mining of full-text biomedical articles and includes two types of subtracks:</P>\
\
<ul>\
<li>Sequences found in publications, grouped by article and searched in genomes with BLAT</li>\
<li>Identifiers in publications that directly relate to chromosome locations (e.g., gene symbols, SNP identifiers, etc)</li>\
</ul>\
<P>Both sources of information are linked to the respective articles.\
Background information on how permission to full-text data was obtained can be found on the <A\
href="http://text.soe.ucsc.edu" target="_blank">project website</A>. \
<H2>Display Convention and Configuration</H2>\
<P>The sequence subtrack indicates the location of sequences in publications\
mapped back to the genome, annotated with the first author and the year of the\
publication.  All matches of one article are grouped ("chained") together.\
Article titles are shown when you move the mouse cursor over the features.\
Thicker parts of the features (exons) represent matching sequences,\
connected by thin lines to matches from the same article within 30 kbp.</P>\
\
<P>The subtrack "individual sequence matches" activates automatically when\
the user clicks a sequence match and follows the link "Show sequence matches individually" \
from the details page.  Mouse-overs show flanking text around the sequence, and clicking\
features links to BLAT alignments.\
</P>\
\
<P>All other subtracks (i.e. bands, genes, SNPs) show the number of matching articles as\
 the feature description.  Clicking on them shows the sentences and sections in articles \
where the identifiers were found.</P>\
\
<P>The track configuration includes a keyword and year filter. Keywords are space-separated\
and are searched in the article's title, author list, and abstract.</P>\
\
<H2>Data</H2>\
<P>The track is based on text from biomedical research articles, obtained as\
part of the <A HREF="http://text.soe.ucsc.edu" target="_blank">UCSC Genocoding Project</A>.</P>\
\
<P>The current dataset consists of about 600,000 files (main text and\
supplementary files) from <A HREF="https://www.ncbi.nlm.nih.gov/pmc/"\
TARGET=_blank>PubMed Central</A> (Open-Access set) and around 6 million text\
files (main text) from <A HREF="https://www.elsevier.com"\
TARGET=_blank>Elsevier</A> (as part of the <A\
HREF="http://www.applications.sciverse.com/action/userhome"\
TARGET=_blank>Sciverse Apps</A> program). </P>\
\
<H2>Methods</H2>\
<P>\
All file types (including XML, raw ASCII, PDFs and various Microsoft\
Office formats (Excel, Word, PowerPoint)) were converted to text. The results were processed \
to find groups of words that look like DNA/RNA sequences or\
words that look like protein sequences. These were then mapped with BLAT to the\
human genome and these model organisms: mouse (mm9), rat (rn4), zebrafish\
(danRer6), <em>Drosophila melanogaster</em> (dm3), <em>X. tropicalis</em> (xenTro2), Medaka\
(oryLat2), <em>C. intestinalis</em> (ci2), <em>C. elegans</em> (ce6) and yeast (sacCer2).\
\
The pipeline roughly proceeds through these steps:\
<UL>\
<LI>For sequences, the best match across all genomes is used, if it is longer than 17 bp and matches at 90% identity. \
Two sets of BLAT parameters are tried, the default ones for sequences longer than 25 bp, very sensitive ones (stepSize=5) for shorter sequences.</LI>\
<LI>Sequences are mapped to genomic DNA. Those that do not match are mapped to RefSeq cDNAs.</LI>\
<LI>Hits from the same article that are closer than 30 kbp are\
joined into one feature (shown as exon-blocks on the browser).</LI>\
<LI>All parts of a joined feature have to match at least 25 bp.</LI>\
<LI>Non-unique hits are kept in the joined feature with the most members.</LI>\
<LI>Joined features with identical members in two different genomes are kept in both genomes.</LI>\
</UL>\
\
<P>Note that due to the 90% identity filter, some sequences do not match\
anywhere in the genome. Examples include primers with added restriction sites,\
mutation primers, or any other sequence that joins or mixes two pieces of genomic\
DNA not part of RefSeq.  Also note that some gene symbols correspond to \
English words which can sometimes lead to many false positives.</P>\
\
<H2>Credits</H2>\
<P>Software and processing by Maximilian Haeussler. UCSC Track visualisation by\
Larry Meyer and Hiram Clawson. Elsevier support by Max Berenstein, Raphael\
Sidi, Judd Dunham, Scott Robbins and colleagues. Original version written at the <A\
HREF="http://bergmanlab.genetics.uga.edu/?page_id=47" target="_blank">Bergman Lab</A>,\
University of Manchester, UK. Testing by Mary Mangan, OpenHelix Inc, and Greg Roe, UCSC.</P>\
\
<H2>Feedback</H2>\
Please send ideas, comments or feedback on this track to\
<A HREF="mailto:&#109;a&#120;&#64;&#115;&#111;&#101;.uc&#115;&#99;.e&#100;&#117;">\
&#109;a&#120;&#64;&#115;&#111;&#101;.uc&#115;&#99;.e&#100;&#117;</A>.\
<!-- above address is max at soe.ucsc.edu -->\
We are very interested in getting access to more articles from publishers for this\
dataset; see the <A HREF="http://text.soe.ucsc.edu" target="_blank">project website</a>.\
</P>\
\
<H2>References</H2>\
<p>\
Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM,\
Open Regulatory Annotation Consortium.\
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-2-r31" target="_blank">\
Text-mining assisted regulatory annotation</a>.\
<em>Genome Biol</em>. 2008;9(2):R31.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18271954" target="_blank">18271954</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374703/" target="_blank">PMC2374703</a>\
</p>\
\
<p>\
Haeussler M, Gerner M, Bergman CM.\
<a href="https://academic.oup.com/bioinformatics/article/27/7/980/230859/Annotating-genes-and-genomes-with-DNA-sequences"\
target="_blank">\
Annotating genes and genomes with DNA sequences extracted from biomedical articles</a>.\
<em>Bioinformatics</em>. 2011 Apr 1;27(7):980-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21325301" target="_blank">21325301</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065681/" target="_blank">PMC3065681</a>\
</p>\
\
<p>\
Van Noorden R.\
<a href="https://www.nature.com/news/trouble-at-the-text-mine-1.10184" target="_blank">\
Trouble at the text mine</a>.\
<em>Nature</em>. 2012 Mar 7;483(7388):134-5.\
</p>\
	pub	1	color 0,0,0\
compositeTrack on\
group pub\
longLabel Publications: Sequences in Scientific Articles\
nextExonText Next Match\
noInherit on\
prevExonText Prev Match\
priority 1\
pubsArticleTable hgFixed.pubsArticle\
pubsMarkerTable hgFixed.pubsMarkerAnnot\
pubsPslTrack pubsBlatPsl\
pubsSequenceTable hgFixed.pubsSequenceAnnot\
shortLabel Publications\
track pubs\
type bed 4\
visibility dense\

snp128	SNPs (128)	bed 6 +	Simple Nucleotide Polymorphisms (dbSNP build 128)	1	1	0	0	0	127	127	127	0	0	0		https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?do_not_redirect&rs=$$	<H2>Description</H2>\
\
<P>\
This track contains information about single nucleotide polymorphisms\
and small insertions and deletions (indels) &mdash; collectively Simple\
Nucleotide Polymorphisms &mdash; from\
<A HREF="https://www.ncbi.nlm.nih.gov/SNP/" target=_blank>dbSNP</A>\
build 128, available from\
<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms" target=_blank>ftp.ncbi.nih.gov/snp</A>.\
</P>\
\
<H2>Interpreting and Configuring the Graphical Display</H2>\
<P>\
  Variants are shown as single tick marks at most zoom levels.\
  When viewing the track at or near base-level resolution, the displayed\
  width of the SNP corresponds to the width of the variant in the reference\
  sequence. Insertions are indicated by a single tick mark displayed between\
  two nucleotides, single nucleotide polymorphisms are displayed as the width \
  of a single base, and multiple nucleotide variants are represented by a \
  block that spans two or more bases.\
</P>\
\
<P>\
  The configuration categories reflect the following definitions (not all categories apply\
  to this assembly):\
</P>\
  <UL>\
\
    <LI>\
      <A name="Class"></A>\
      <B>Class</B>: Describes the observed alleles<BR>\
      <UL>\
        <LI><B>Single</B> - single nucleotide variation: all observed alleles are single nucleotides\
\	    (can have 2, 3 or 4 alleles)\
        <LI><B>In-del</B> - insertion/deletion\
        <LI><B>Heterozygous</B> - heterozygous (undetermined) variation: allele contains string '(heterozygous)'\
        <LI><B>Microsatellite</B> - the observed allele from dbSNP is variation in counts of short tandem repeats\
        <LI><B>Named</B> - the observed allele from dbSNP is given as a text name\
        <LI><B>No Variation</B> - no variation asserted for sequence\
        <LI><B>Mixed</B> - the cluster contains submissions from multiple classes\
        <LI><B>Multiple Nucleotide Polymorphism</B> - alleles of the same length, length > 1, and from set of {A,T,C,G}\
        <LI><B>Insertion</B> - the polymorphism is an insertion relative to the reference assembly\
        <LI><B>Deletion</B> - the polymorphism is a deletion relative to the reference assembly\
        <LI><B>Unknown</B> - no classification provided by data contributor\
      </UL>\
    </LI>\
\
\
    <LI>\
      <A name="Valid"></A>\
      <B><A HREF="https://www.ncbi.nlm.nih.gov/SNP/snp_legend.cgi?legend=validation" \
\	target="_blank">Validation</A></B>: Method used to validate\
\	the variant (<I>each variant may be validated by more than one method</I>)<BR>\
        <UL>\
        <LI><B>By Frequency</B> - at least one submitted SNP in cluster has frequency data submitted\
        <LI><B>By Cluster</B> - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method\
        <LI><B>By Submitter</B> - at least one submitter SNP in cluster was validated by independent assay\
        <LI><B>By 2 Hit/2 Allele</B> - all alleles have been observed in at least 2 chromosomes\
        <LI><B>By HapMap</B> - validated by HapMap project\
        <LI><B>Unknown</B> - no validation has been reported for this variant\
      </UL>\
    </LI>\
    <LI>\
      <A name="Func"></A>\
      <B>Function</B>: dbSNP's predicted functional effect of variant on RefSeq transcripts,\
      both curated (NM_* and NR_*) as in the RefSeq Genes track and predicted (XM_* and XR_*),\
      not shown in UCSC Genome Browser.\
      A variant may have more than one functional role if it overlaps\
      multiple transcripts.\
      As of dbSNP build 128, several functional terms have been replaced by\
      more detailed functional terms;\
      for filtering and coloring, the new function terms are grouped into more\
      general categories:<BR>\
      <UL>\
        <LI><B>Locus Region</B> - variation is 3' to and within 500  bases of a\
            transcript, or is 5' to and within 2000 bases of a transcript\
\	    (dbSNP terms: <TT>near-gene-3</TT> and <TT>near-gene-5</TT>\
\	    replace older term <TT>locus</TT>;\
\	    Sequence Ontology terms:\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001632"\
\	    TARGET=_BLANK>downstream_gene_variant</A></TT>,\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001631"\
\	    TARGET=_BLANK>upstream_gene_variant</A></TT>)</LI>\
        <LI><B>Coding - Synonymous</B> - no change in peptide for allele with\
\	    respect to reference assembly\
\	    (dbSNP term: <TT>coding-synon</TT>;\
\	    Sequence Ontology term:\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001819"\
\	    TARGET=_BLANK>synonymous_variant</A></TT>)</LI>\
        <LI><B>Coding - Non-Synonymous</B> - change in peptide for allele with\
\	    respect to reference assembly\
\	    (dbSNP terms: <TT>nonsense</TT>, <TT>missense</TT>, <TT>frameshift</TT>\
\	    replace older term <TT>coding-nonsynon</TT>;\
\	    Sequence Ontology terms:\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001587"\
\	    TARGET=_BLANK>stop_gained</A></TT>,\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001583"\
\	    TARGET=_BLANK>missense_variant</A></TT>,\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001589"\
\	    TARGET=_BLANK>frameshift_variant</A></TT>)</LI>\
        <LI><B>Untranslated</B> - variation in transcript, but not in coding\
\	    region interval\
\	    (dbSNP terms: <TT>untranslated-3</TT>, <TT>untranslated-5</TT>\
\	    replace older term <TT>untranslated</TT>;\
\	    Sequence Ontology terms:\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001624"\
\	    TARGET=_BLANK>3_prime_UTR_variant</A></TT>,\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001623"\
\	    TARGET=_BLANK>5_prime_UTR_variant</A></TT>)</LI>\
        <LI><B>Intron</B> - variation in intron, but not in first two or last two bases of intron\
\	    (dbSNP term: <TT>intron</TT>;\
\	    Sequence Ontology term:\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001627"\
\	    TARGET=_BLANK>intron_variant</A></TT>)</LI>\
        <LI><B>Splice Site</B> - variation in first two or last two bases of intron\
\	    (dbSNP terms: <TT>splice-3</TT>, <TT>splice-5</TT>\
\	    replace older term <TT>splice-site</TT>;\
\	    Sequence Ontology terms:\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001574"\
\	    TARGET=_BLANK>splice_acceptor_variant</A></TT>,\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001575"\
\	    TARGET=_BLANK>splice_donor_variant</A></TT>)</LI>\
        <LI><B>Reference (coding)</B> - one of the observed alleles of a SNP\
\	    in a coding region matches the reference assembly\
\	    (dbSNP term: <TT>cds-reference</TT>;\
\	    Sequence Ontology term:\
\	    <TT><A HREF="http://sequenceontology.org/browser/current_release/term/SO:0001580"\
\	    TARGET=_BLANK>coding_sequence_variant</A></TT>)</LI>\
        <LI><B>Unknown</B> - no known functional classification</LI>\
      </UL>\
    </LI>\
    <LI>\
      <A name="MolType"></A>\
      <B>Molecule Type</B>: Sample used to find this variant<BR>\
      <UL>\
        <LI><B>Genomic</B> - variant discovered using a genomic template\
        <LI><B>cDNA</B> - variant discovered using a cDNA template\
        <LI><B>Unknown</B> - sample type not known\
      </UL>\
    </LI>\
    <LI>\
      <A name="AvHet"></A>\
      <B>Average heterozygosity</B>: Calculated by dbSNP as described \
      <A HREF="https://www.ncbi.nlm.nih.gov/SNP/Hetfreq.html" target=_blank>here</A>\
      <UL>\
      <LI> Average heterozygosity should not exceed 0.5 for bi-allelic \
           single-base substitutions.\
      </UL>\
    </LI>\
    <LI>\
      <A name="Weight"></A>\
      <B>Weight</B>: Alignment quality assigned by dbSNP<BR>\
      <UL>\
      <LI>Weight can be 0, 1, 2, 3 or 10.   \
      <LI>Weight = 1 are the highest quality alignments.\
      <LI>Weight = 0 and weight = 10 are excluded from the data set.\
      <LI>A filter on maximum weight value is supported, which defaults to 3.\
      </UL>\
    </LI>\
  </UL>\
\
 <P>\
 You can configure this track such that the details page displays\
 the function and coding differences relative to\
 particular gene sets.  Choose the gene sets from the list on the SNP\
 configuration page displayed beneath this heading: <EM>On details page,\
 show function and coding differences relative to</EM>.\
 When one or more gene tracks are selected, the SNP details page\
 lists all genes that the SNP hits (or is close to), with the same keywords\
 used in the <A HREF="#Func">function</A> category.  The function usually\
 agrees with NCBI's function, but can sometimes give a bit more detail\
 (e.g. more detail about how close a near-gene SNP is to a nearby gene).\
 </P>\
\
<H2>Insertions/Deletions</H2>\
<P>\
dbSNP uses a class called 'in-del'.  We compare the length of the\
reference allele to the length(s) of observed alleles; if the\
reference allele is shorter than all other observed alleles, we change\
'in-del' to 'insertion'.  Likewise, if the reference allele is longer\
than all other observed alleles, we change 'in-del' to 'deletion'.\
</P>\
\
<H2>UCSC Annotations</H2>\
<P>\
UCSC checks for several unusual conditions that may indicate a problem \
with the mapping, and reports them in the Annotations section if found:\
</P>\
  <UL>\
  <LI>The dbSNP reference allele is not the same as the UCSC reference\
      allele, i.e. the bases in the mapped position range.</LI>\
  <LI>Class is single, in-del, mnp or mixed and the UCSC reference\
      allele does not match any observed allele.</LI>\
  <LI>In NCBI's alignment of flanking sequences to the genome, part\
      of the flanking sequence around the SNP does not align to\
      the genome.</LI>\
  <LI>Class is single, but the size of the mapped SNP is not one base.</LI>\
  <LI>Class is named and indicates an insertion or deletion, but the size\
      of the mapped SNP implies otherwise.</LI>\
  <LI>Class is single and the format of observed alleles is unexpected.</LI>\
  <LI>The length of the observed allele(s) is not available because it is\
      too long.</LI>\
  <LI>Multiple distinct insertion SNPs have been mapped to this location.</LI>\
  <LI>At least one observed allele contains an ambiguous \
      <A HREF=../goldenPath/help/iupac.html>IUPAC</A> base (e.g. R, Y, N).</LI>\
  </UL>\
\
Another condition, which does not necessarily imply any problem, is noted:\
  <UL>\
  <LI>Class is single and SNP is tri-allelic or quad-allelic.</LI>\
  </UL>\
\
<H2>UCSC Re-alignment of flanking sequences</H2>\
<P>\
dbSNP determines the genomic locations of SNPs by aligning their flanking \
sequences to the genome.\
UCSC displays SNPs in the locations determined by dbSNP, but does not\
have access to the alignments on which dbSNP based its mappings.\
Instead, UCSC re-aligns the flanking sequences \
to the neighboring genomic sequence for display on SNP details pages.  \
While the recomputed alignments may differ from dbSNP's alignments,\
they often are informative when UCSC has annotated an unusual condition.\
</P>\
\
<H2>Data Sources</H2>\
<P>\
The data that comprise this track were extracted from database dump files \
and headers of fasta files downloaded from NCBI.  \
The database dump files were downloaded from \
<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/"\
TARGET=_BLANK>ftp://ftp.ncbi.nih.gov/snp/organisms/</A>\
<EM>organism</EM>_<EM>tax_id</EM>/database/\
(e.g. for Human, <EM>organism</EM>_<EM>tax_id</EM> = human_9606).\
The fasta files were downloaded from \
<A HREF="ftp://ftp.ncbi.nih.gov/snp/organisms/"\
TARGET=_BLANK>ftp://ftp.ncbi.nih.gov/snp/organisms/</A>\
<EM>organism</EM>_<EM>tax_id</EM>/rs_fasta/\
</P>\
  <UL>\
  <LI>Coordinates, orientation, location type and dbSNP reference allele data\
      were obtained from b128_SNPContigLoc_36_2.bcp.gz and \
      b128_SNPContigInfo_36_2.bcp.gz.  \
  <LI>b128_SNPMapInfo_36_2.bcp.gz provided the alignment weights.\
  <LI>Functional classification was obtained from \
      b128_SNPContigLocusId_36_2.bcp.gz. The internal database representation\
      uses dbSNP's function terms, but for display in SNP details pages,\
      these are translated into\
      <A HREF="http://www.sequenceontology.org/"\
      TARGET=_BLANK>Sequence Ontology</A> terms.\
  <LI>Validation status and heterozygosity were obtained from SNP.bcp.gz.\
  <LI>The header lines in the rs_fasta files were used for molecule type,\
      class and observed polymorphism.\
  </UL>\
\
<H2>Data Access</H2>\
<p>\
<b>Note:</b> It is not recommeneded to use LiftOver to convert SNPs between assemblies,\
and more information about how to convert SNPs between assemblies can be found on the following\
<a href="/FAQ/FAQreleases.html#snpConversion">FAQ entry</a>.</p>\
<P>\
The raw data can be explored interactively with the <A HREF="../../cgi-bin/hgTables"TARGET=_blank>Table Browser</a>,\
<A HREF="../../cgi-bin/hgIntegrator"TARGET=_blank>Data Integrator</a>, or <A HREF="../../cgi-bin/hgVai"TARGET=_blank>Variant Annotation Integrator</a>.\
For automated analysis, the genome annotation can be downloaded from the downloads server for <A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/"TARGET=_blank>mm9</a> and\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/"TARGET=_blank>hg18</a> (snp128*.txt.gz) or the <A HREF="../goldenPath/help/mysql.html"TARGET=_blank>public MySQL server</a>.\
Please refer to our <A HREF="https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!search/download+snps"TARGET=_blank>mailing list archives</a>\
for questions and example queries, or our <A HREF="../FAQ/FAQdownloads.html#download36"TARGET=_blank>Data Access FAQ</a> for more information.\
</P>\
\
<H2>Orthologous Alleles (human only)</H2>\
<P>\
Beginning with the March 2006 human assembly, we provide a related table that \
contains orthologous alleles in the chimpanzee and rhesus macaque assemblies.\
We use our liftOver utility to identify the orthologous alleles.  The candidate human SNPs are \
a filtered list that meet the criteria:\
<UL>\
<LI>class = 'single'\
<LI>chromEnd = chromStart + 1\
<LI>align to just one location\
<LI>are not aligned to a chrN_random chrom\
<LI>are biallelic (not tri or quad allelic)\
</UL>\
\
In some cases the orthologous allele is unknown; these are set to 'N'.\
If a lift was not possible, we set the orthologous allele to '?' and the \
orthologous start and end position to 0 (zero).\
\
<H2>Masked FASTA Files (human only)</H2>\
\
FASTA files that have been modified to use \
<A HREF=../goldenPath/help/iupac.html>IUPAC</A>\
ambiguous nucleotide characters at\
each base covered by a single-base substitution are available for download\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/hg18/snp128Mask/">here</A>.\
Note that only single-base substitutions (no insertions or deletions) were used\
to mask the sequence, and these were filtered to exlcude problematic SNPs.\
\
<H2>References</H2>\
<P>\
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. \
<A HREF="https://academic.oup.com/nar/article/29/1/308/1116004" TARGET=_blank>\
dbSNP: the NCBI database of genetic variation</A>.\
<em>Nucleic Acids Res</em>. 2001 Jan 1;29(1):308-11.\
	varRep	1	group varRep\
longLabel Simple Nucleotide Polymorphisms (dbSNP build 128)\
maxWindowToDraw 10000000\
priority 1\
shortLabel SNPs (128)\
track snp128\
type bed 6 +\
url https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?do_not_redirect&rs=$$\
urlLabel dbSNP:\
visibility dense\

stsMapMouseNew	STS Markers	bed 5 +	STS Markers on Genetic and Radiation Hybrid Maps	1	1	0	0	0	128	128	255	0	0	0			<H2>Description</H2>\
<P>This track shows locations of Sequence Tagged Sites (STS) \
along the mouse draft assembly.  These markers have been mapped using \
either genetic mapping (<A href="https://www.broadinstitute.org/science/projects/mammals-models/mouse/old-mouse-genome-data"\
TARGET=_blank>WICGR Mouse Genetic Map</A>, <A href="http://www.informatics.jax.org/"\
TARGET=_blank>MGD Genetic Map</A>) or radiation hybridization mapping\
(<A href="https://www.broadinstitute.org/mouse_rh/index.html" \
TARGET=_blank>Whitehead/MRC RH Map</A>) techniques.</p>  \
\
Additional data on the individual maps can be found at the following links:\
<UL>\
<LI>NCBI UniSTS\
<LI><A href="http://www.informatics.jax.org" TARGET=_blank> Mouse Genome Informatics (MGI)</A>\
</UL>\
\
<P>By default all genetic map markers are shown as blue; only radiation \
hybrid markers and markers that are neither genetic nor radiation hybrid \
are shown as black; markers that map to more than one position are \
shown in lighter colors. Users  can choose a color to highlight a subset \
of markers of interest from the Filter options in STS Markers \
Track Setting page.\
\
<H2>Methods</H2>\
<P>Positions of STS markers are determined using both full sequences\
and primer information.  Full sequences are aligned using <A\
HREF="https://genome.cshlp.org/content/12/4/656.full" TARGET=_blank>blat</A>,\
while <A\
HREF="https://www.ncbi.nlm.nih.gov/sutils/e-pcr/"\
TARGET = _BLANK">ePCR</A> is used to find locations using primer information.\
\
<H2>Using the Filter</H2>\
<P>The track filter can be used to change the color or include/exclude\
a set of map data within the track. This is helpful when many items\
are shown in the track display, especially when only some are relevant\
to the current task. To use the filter:\
<UL>\
<LI>In the pulldown menu, select the map whose data you would like to\
highlight or exclude in the display. By default, the &quot;All\
Genetic&quot; option is selected.\
<LI>Choose the color or display characteristic that will be used to\
highlight or include/exclude the filtered items. If\
&quot;exclude&quot; is chosen, the browser will not display data from\
the map selected in the pulldown list. If &quot;include&quot; is\
selected, the browser will display only data from the selected map.\
</UL></P>\
<P>When you have finished configuring the filter, click the\
<em>Submit</em> button.</P>\
\
<H2>Credits</H2>\
<P> This track was designed and implemented by Terry Furey and Yontao Lu. Many thanks to\
<A HREF="https://www.broadinstitute.org/" TARGET=_blank>Whitehead Institute (Broad Institute)</A>\
 and <A HREF="https://www.jax.org/" TARGET=_blank>Jackson Lab</A> for \
contributing the data.\
	map	1	altColor 128,128,255,\
group map\
longLabel STS Markers on Genetic and Radiation Hybrid Maps\
priority 1\
shortLabel STS Markers\
track stsMapMouseNew\
type bed 5 +\
visibility dense\

knownGene	UCSC Genes	genePred knownGenePep knownGeneMrna	UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics)	3	1	12	12	120	133	133	187	0	0	0			<H2>Description</H2>\
<P>\
The UCSC Genes track shows gene predictions based on data\
from RefSeq, GenBank, and the <a href="hgTrackUi?db=mm9&g=tRNAs">tRNA Genes</a>\
track. This is a moderately conservative set of\
predictions, requiring the support of one GenBank RNA sequence plus\
at least one additional line of evidence. The RefSeq RNAs are an exception to \
this, requiring no additional evidence. The track includes both protein-coding\
and putative non-coding transcripts. Some of these non-coding transcripts may \
actually code for protein, but the evidence for the associated protein is weak\
at best. Compared to RefSeq, this gene set has generally about 10% more \
protein-coding genes, approximately five times as many putative non-coding \
genes, and \
about twice as many splice variants.</P>\
\
<p>\
For more information on the different gene tracks, see our <a target=_blank \
href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>\
\
<H2>Display Conventions and Configuration</H2>\
<P>\
This track in general follows the display conventions for\
<A HREF="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction\
tracks</A>.  The exons for putative noncoding genes and untranslated regions \
are represented by relatively thin blocks, while those for coding open \
reading frames are thicker.  The following color key is used:\
<UL>\
<LI>Black -- feature has a corresponding entry in the Protein Databank (PDB)\
<LI>Dark blue -- transcript has been reviewed or validated by either the \
RefSeq or SwissProt staff\
<LI>Medium blue -- other RefSeq transcripts\
<LI>Light blue -- non-RefSeq transcripts\
</UL></P>\
<P>\
This track contains an optional codon coloring\
feature that allows users to quickly validate and compare gene predictions.\
To display codon colors, select the <em>genomic codons</em> option from the\
<em>Color track by codons</em> pull-down menu. Click\
<A HREF="../goldenPath/help/hgCodonColoring.html">here</A> for more\
information about this feature. </P>\
\
<H2>Methods</H2>\
<P>\
The UCSC Genes are built using a multi-step pipeline:  \
<OL>\
<LI>RefSeq and GenBank RNAs are aligned to the genome with BLAT, keeping \
only the best \
alignments for each RNA and discarding alignments of less than 98% identity.\
<LI>Alignments are broken up at non-intronic gaps, with small isolated \
fragments thrown out.\
<LI>A splicing graph is created for each set of overlapping alignments. This \
graph \
has an edge for each exon or intron, and a vertex for each splice site, start, \
and end.\
Each RNA that contributes to an edge is kept as evidence for that edge.\
<LI>A similar splicing graph is created in the mouse, based on mouse RNA and \
ESTs. If\
the mouse graph has an edge that is orthologous to an edge in the human graph, \
that is added to the evidence for the human edge.\
<LI>If an edge in the splicing graph is supported by two or more human ESTs, \
it is added as evidence for the edge.\
<LI>If there is an Exoniphy prediction for an exon, that is added as evidence.\
<LI>The graph is traversed to generate all unique transcripts. The traversal is \
guided by the initial RNAs to avoid a combinatorical explosion in alternative \
splicing. All refSeq transcripts are output. For other multi-exon transcripts\
to be output, an edge supported by at least one additional line of evidence \
beyond the RNA is required.  Single-exon genes require either two RNAs or two \
additional lines of evidence beyond the single RNA. \
<LI>Protein predictions are generated. For non-RefSeq transcripts we use the \
txCdsPredict program to determine if the transcript is protein-coding and if so,\
the locations of the start and stop codons. \
The program weighs as positive evidence the length of the protein, the \
presence of a Kozak consensus sequence at the start codon, and the length of \
the orthologous predicted protein in other species.\
As negative evidence it considers nonsense-mediated decay and start codons in \
any frame upstream of the predicted start codon. For RefSeq transcripts \
the RefSeq protein prediction is used.\
<LI>The corresponding UniProt protein is found, if any.\
<LI>The transcript is assigned a permanent "uc" accession.\
</OL>\
\
<H2>Credits</H2>\
<P>\
The UCSC Genes track was produced at UCSC using a computational pipeline\
developed by Jim Kent, Chuck Sugnet and Mark Diekhans.  \
It is based on data from NCBI\
<A HREF="https://www.ncbi.nlm.nih.gov/refseq/" TARGET=_blank>RefSeq</A>,\
<A HREF="https://www.uniprot.org/" TARGET=_blank>UniProt</A> \
(including TrEMBL and TrEMBL-NEW) and \
<A HREF="https://www.ncbi.nlm.nih.gov/genbank/"\
TARGET=_blank>GenBank</A>. Our thanks to the people running these databases\
and to the scientists worldwide who have made contributions to them. </P>\
\
<H2>Data Use Restrictions</H2>\
<P>\
The UniProt data have the following terms of use, UniProt copyright(c) 2002 - \
2004 UniProt consortium:</P>\
<P>\
For non-commercial use, all databases and documents in the UniProt FTP\
directory may be copied and redistributed freely, without advance\
permission, provided that this copyright statement is reproduced with\
each copy.</P>\
<P>\
For commercial use, all databases and documents in the UniProt FTP\
directory except the files\
<UL>\
<LI>ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz\
<LI>ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.xml.gz\
</UL>\
may be copied and redistributed freely, without advance permission,\
provided that this copyright statement is reproduced with each copy.\
More information for commercial users can be found \
<A HREF="https://www.uniprot.org/help/license" TARGET=_blank>here</A>.\
<P>\
From January 1, 2005, all databases and documents in the UniProt FTP\
directory may be copied and redistributed freely by all entities,\
without advance permission, provided that this copyright statement is\
reproduced with each copy.</P>\
\
<H2>References</H2>\
<p>\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
<a href="https://academic.oup.com/nar/article/32/suppl_1/D23/2505202" target="_blank">\
GenBank: update</a>.\
<em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D23-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681350" target="_blank">14681350</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308779/" target="_blank">PMC308779</a>\
</p>\
\
<p>\
Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D.\
<a href="https://academic.oup.com/bioinformatics/article/22/9/1036/200093"\
target="_blank">\
The UCSC Known Genes</a>.\
<em>Bioinformatics</em>. 2006 May 1;22(9):1036-46.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16500937" target="_blank">16500937</a>\
</p>\
\
<p>\
Kent WJ.\
<a href="https://genome.cshlp.org/content/12/4/656.full" target="_blank">\
BLAT--the BLAST-like alignment tool</a>.\
<em>Genome Res</em>. 2002 Apr;12(4):656-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a>\
</p>\
	genes	1	baseColorDefault genomicCodons\
baseColorUseCds given\
bigGeneDataUrl /gbdb/mm9/knownGene.bb\
color 12,12,120\
defaultLinkedTables kgXref\
directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s\
exonNumbers on\
group genes\
hgGene on\
hgsid on\
idXref kgAlias kgID alias\
intronGap 12\
longLabel UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics)\
priority 1\
shortLabel UCSC Genes\
track knownGene\
type genePred knownGenePep knownGeneMrna\
visibility pack\

refGene	UCSC RefSeq	genePred refPep refMrna	UCSC annotations of RefSeq RNAs (NM_* and NR_*)	1	1	12	12	120	133	133	187	0	0	0			<h2>Description</h2>\
\
<p>\
The RefSeq Genes track shows known mouse protein-coding and\
non-protein-coding genes taken from the NCBI RNA reference sequences\
collection (RefSeq). The data underlying this track are updated weekly.</p>\
\
<p>\
Please visit the <a href="https://www.ncbi.nlm.nih.gov/projects/RefSeq/update.cgi"\
target="_blank">Feedback for Gene and Reference Sequences (RefSeq)</a> page to\
make suggestions, submit additions and corrections, or ask for help concerning\
RefSeq records.\
</p>\
\
<p>\
For more information on the different gene tracks, see our <a target=_blank \
href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track follows the display conventions for\
<a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay" target="_blank">\
gene prediction tracks</a>.\
The color shading indicates the level of review the RefSeq record has\
undergone: predicted (light), provisional (medium), reviewed (dark).\
</p>\
\
<p>\
The item labels and display colors of features within this track can be\
configured through the controls at the top of the track description page.\
<ul>\
<li><b>Label:</b> By default, items are labeled by gene name. Click the\
appropriate Label option to display the accession name instead of the gene\
name, show both the gene and accession names, or turn off the label\
completely.</li>\
<li><b>Codon coloring:</b> This track contains an optional codon coloring\
feature that allows users to quickly validate and compare gene predictions.\
To display codon colors, select the <em>genomic codons</em> option from the\
<em>Color track by codons</em> pull-down menu. For more information about this\
feature, go to the\
<a href="../goldenPath/help/hgCodonColoring.html" TARGET="_blank">\
Coloring Gene Predictions and Annotations by Codon</a> page.</li>\
<li><b>Hide non-coding genes:</b> By default, both the protein-coding and\
non-protein-coding genes are displayed.  If you wish to see only the coding\
genes, click this box.</li>\
</ul>\
</p>\
\
<h2>Methods</h2>\
\
<p>\
RefSeq RNAs were aligned against the mouse genome using BLAT.  Those\
with an alignment of less than 15% were discarded. When a single RNA\
aligned in multiple places, the alignment having the highest base identity\
was identified.  Only alignments having a base identity level within 0.1% of\
the best and at least 96% base identity with the genomic sequence were kept.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
This track was produced at UCSC from RNA sequence data generated by scientists\
worldwide and curated by the NCBI\
<a href="https://www.ncbi.nlm.nih.gov/refseq/" target="_blank">RefSeq project</a>.\
</p>\
\
<h2>References</h2>\
\
<p>\
Kent WJ.\
<a href="https://genome.cshlp.org/content/12/4/656.full" target="_blank">\
BLAT - the BLAST-like alignment tool</a>.\
<em>Genome Res.</em> 2002 Apr;12(4):656-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a>\
</p>\
\
<p>\
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,\
Landrum MJ, McGarvey KM <em>et al</em>.\
<a href="https://academic.oup.com/nar/article/42/D1/D756/1051112/RefSeq-an-update-on-mammalian-reference-sequences" target="_blank">\
RefSeq: an update on mammalian reference sequences</a>.\
<em>Nucleic Acids Res</em>. 2014 Jan;42(Database issue):D756-63.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24259432" target="_blank">24259432</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965018/" target="_blank">PMC3965018</a>\
</p>\
\
<p>\
Pruitt KD, Tatusova T, Maglott DR.\
<a href="https://academic.oup.com/nar/article/33/suppl_1/D501/2505241/NCBI-Reference-Sequence-RefSeq-a-curated-non" target="_blank">\
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins</a>.\
<em>Nucleic Acids Res.</em> 2005 Jan 1;33(Database issue):D501-4.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15608248" target="_blank">15608248</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979/" target="_blank">PMC539979</a>\
</p>\
	genes	1	baseColorDefault genomicCodons\
baseColorUseCds given\
color 12,12,120\
dataVersion \
group genes\
idXref hgFixed.refLink mrnaAcc name\
longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*)\
parent refSeqComposite off\
priority 4\
shortLabel UCSC RefSeq\
track refGene\
type genePred refPep refMrna\
visibility dense\

vegaGene	Vega Protein Genes	genePred vegaPep	Vega Protein Coding Annotations	0	1	0	50	225	127	152	240	0	0	21	chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY,	http://vega.sanger.ac.uk/Mus_musculus/transview?transcript=$$		genes	1	color 0,50,225\
longLabel Vega Protein Coding Annotations\
parent vegaGeneComposite\
priority 1\
shortLabel Vega Protein Genes\
track vegaGene\

netRn4	Rat Net	netAlign rn4 chainRn4	Rat (Nov. 2004 (Baylor 3.4/rn4)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of rat (Nov. 2004 (Baylor 3.4/rn4)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
rat and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
rat assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best rat/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The rat sequence used in this annotation is from\
the Nov. 2004 (Baylor 3.4/rn4) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the rat/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single rat chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>56</TD><TD>-109</TD><TD>-45</TD><TD>-137</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-109</TD><TD>100</TD><TD>-103</TD><TD>-45</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-45</TD><TD>-103</TD><TD>100</TD><TD>-109</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-137</TD><TD>-45</TD><TD>-109</TD><TD>56</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Rat (Nov. 2004 (Baylor 3.4/rn4)) Alignment Net\
parent chainNetRn4Viewnet\
shortLabel Rat Net\
subGroups view=net\
track netRn4\
type netAlign rn4 chainRn4\

netBraFlo1	Lancelet Net	netAlign braFlo1 chainBraFlo1	Lancelet (Mar. 2006 (JGI 1.0/braFlo1)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of lancelet (Mar. 2006 (JGI 1.0/braFlo1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
lancelet and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
lancelet assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best lancelet/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The lancelet sequence used in this annotation is from\
the Mar. 2006 (JGI 1.0/braFlo1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the lancelet/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single lancelet chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Lancelet (Mar. 2006 (JGI 1.0/braFlo1)) Alignment Net\
parent chainNetBraFlo1Viewnet\
shortLabel Lancelet Net\
subGroups view=net\
track netBraFlo1\
type netAlign braFlo1 chainBraFlo1\

netOryLat2	Medaka Net	netAlign oryLat2 chainOryLat2	Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) Alignment Net	2	2	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
medaka and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
medaka assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best medaka/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The medaka sequence used in this annotation is from\
the Oct. 2005 (NIG/UT MEDAKA1/oryLat2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the medaka/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single medaka chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) Alignment Net\
otherDb oryLat2\
parent chainNetOryLat2Viewnet\
shortLabel Medaka Net\
subGroups view=net\
track netOryLat2\
type netAlign oryLat2 chainOryLat2\

netLoxAfr3	Elephant Net	netAlign loxAfr3 chainLoxAfr3	Elephant (Jul. 2009 (Broad/loxAfr3)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of elephant (Jul. 2009 (Broad/loxAfr3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
elephant and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
elephant assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best elephant/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The elephant sequence used in this annotation is from\
the Jul. 2009 (Broad/loxAfr3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the elephant/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single elephant chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Elephant (Jul. 2009 (Broad/loxAfr3)) Alignment Net\
parent chainNetLoxAfr3Viewnet\
shortLabel Elephant Net\
subGroups view=net\
track netLoxAfr3\
type netAlign loxAfr3 chainLoxAfr3\

netEquCab2	Horse Net	netAlign equCab2 chainEquCab2	Horse (Sep. 2007 (Broad/equCab2)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of horse (Sep. 2007 (Broad/equCab2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
horse and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
horse assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best horse/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The horse sequence used in this annotation is from\
the Sep. 2007 (Broad/equCab2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the horse/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single horse chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Horse (Sep. 2007 (Broad/equCab2)) Alignment Net\
parent chainNetEquCab2Viewnet\
shortLabel Horse Net\
subGroups view=net\
track netEquCab2\
type netAlign equCab2 chainEquCab2\

netCavPor3	Guinea pig Net	netAlign cavPor3 chainCavPor3	Guinea pig (Feb. 2008 (Broad/cavPor3)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of guinea pig (Feb. 2008 (Broad/cavPor3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
guinea pig and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
guinea pig assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best guinea pig/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The guinea pig sequence used in this annotation is from\
the Feb. 2008 (Broad/cavPor3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the guinea pig/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single guinea pig chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Guinea pig (Feb. 2008 (Broad/cavPor3)) Alignment Net\
parent chainNetCavPor3Viewnet\
shortLabel Guinea pig Net\
subGroups view=net\
track netCavPor3\
type netAlign cavPor3 chainCavPor3\

netRheMac2	Rhesus Net	netAlign rheMac2 chainRheMac2	Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) Alignment net	2	2	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
rhesus and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
rhesus assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best rhesus/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The rhesus sequence used in this annotation is from\
the Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the rhesus/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single rhesus chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) Alignment net\
parent chainNetRheMac2Viewnet\
shortLabel Rhesus Net\
subGroups view=net\
track netRheMac2\
type netAlign rheMac2 chainRheMac2\

netAilMel1	Panda Net	netAlign ailMel1 chainAilMel1	Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
panda and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
panda assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best panda/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The panda sequence used in this annotation is from\
the Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the panda/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single panda chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) Alignment Net\
parent chainNetAilMel1Viewnet\
shortLabel Panda Net\
subGroups view=net\
track netAilMel1\
type netAlign ailMel1 chainAilMel1\

netGalGal3	Chicken Net	netAlign galGal3 chainGalGal3	Chicken (May 2006 (WUGSC 2.1/galGal3)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of chicken (May 2006 (WUGSC 2.1/galGal3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
chicken and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
chicken assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best chicken/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The chicken sequence used in this annotation is from\
the May 2006 (WUGSC 2.1/galGal3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the chicken/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single chicken chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Chicken (May 2006 (WUGSC 2.1/galGal3)) Alignment Net\
parent chainNetGalGal3Viewnet\
shortLabel Chicken Net\
subGroups view=net\
track netGalGal3\
type netAlign galGal3 chainGalGal3\

netDanRer7	Zebrafish Net	netAlign danRer7 chainDanRer7	Zebrafish (Jul. 2010 (Zv9/danRer7)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of zebrafish (Jul. 2010 (Zv9/danRer7)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
zebrafish and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
zebrafish assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best zebrafish/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The zebrafish sequence used in this annotation is from\
the Jul. 2010 (Zv9/danRer7) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the zebrafish/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single zebrafish chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Zebrafish (Jul. 2010 (Zv9/danRer7)) Alignment Net\
parent chainNetDanRer7Viewnet\
shortLabel Zebrafish Net\
subGroups view=net\
track netDanRer7\
type netAlign danRer7 chainDanRer7\

netAnoCar2	Lizard Net	netAlign anoCar2 chainAnoCar2	Lizard (May 2010 (Broad AnoCar2.0/anoCar2)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of lizard (May 2010 (Broad AnoCar2.0/anoCar2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
lizard and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
lizard assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best lizard/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The lizard sequence used in this annotation is from\
the May 2010 (Broad AnoCar2.0/anoCar2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the lizard/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single lizard chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Lizard (May 2010 (Broad AnoCar2.0/anoCar2)) Alignment Net\
parent chainNetAnoCar2Viewnet\
shortLabel Lizard Net\
subGroups view=net\
track netAnoCar2\
type netAlign anoCar2 chainAnoCar2\

netCanFam2	Dog Net	netAlign canFam2 chainCanFam2	Dog (May 2005 (Broad/canFam2)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of dog (May 2005 (Broad/canFam2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
dog and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
dog assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best dog/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The dog sequence used in this annotation is from\
the May 2005 (Broad/canFam2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the dog/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single dog chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Dog (May 2005 (Broad/canFam2)) Alignment Net\
parent chainNetCanFam2Viewnet\
shortLabel Dog Net\
subGroups view=net\
track netCanFam2\
type netAlign canFam2 chainCanFam2\

netMelGal1	Turkey Net	netAlign melGal1 chainMelGal1	Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
turkey and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
turkey assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best turkey/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The turkey sequence used in this annotation is from\
the Dec. 2009 (TGC Turkey_2.01/melGal1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the turkey/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single turkey chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) Alignment Net\
parent chainNetMelGal1Viewnet\
shortLabel Turkey Net\
subGroups view=net\
track netMelGal1\
type netAlign melGal1 chainMelGal1\

netOviAri1	Sheep Net	netAlign oviAri1 chainOviAri1	Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
sheep and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
sheep assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best sheep/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The sheep sequence used in this annotation is from\
the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the sheep/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single sheep chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) Alignment Net\
parent chainNetOviAri1Viewnet\
shortLabel Sheep Net\
subGroups view=net\
track netOviAri1\
type netAlign oviAri1 chainOviAri1\

netGasAcu1	Stickleback Net	netAlign gasAcu1 chainGasAcu1	Stickleback (Feb. 2006 (Broad/gasAcu1)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of stickleback (Feb. 2006 (Broad/gasAcu1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
stickleback and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
stickleback assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best stickleback/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The stickleback sequence used in this annotation is from\
the Feb. 2006 (Broad/gasAcu1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the stickleback/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single stickleback chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Stickleback (Feb. 2006 (Broad/gasAcu1)) Alignment Net\
parent chainNetGasAcu1Viewnet\
shortLabel Stickleback Net\
subGroups view=net\
track netGasAcu1\
type netAlign gasAcu1 chainGasAcu1\

netXenTro3	X. tropicalis Net	netAlign xenTro3 chainXenTro3	X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
X. tropicalis and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
X. tropicalis assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best X. tropicalis/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The X. tropicalis sequence used in this annotation is from\
the Nov. 2009 (JGI 4.2/xenTro3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the X. tropicalis/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single X. tropicalis chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) Alignment Net\
parent chainNetXenTro3Viewnet\
shortLabel X. tropicalis Net\
subGroups view=net\
track netXenTro3\
type netAlign xenTro3 chainXenTro3\

netFelCat4	Cat Net	netAlign felCat4 chainFelCat4	Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
cat and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
cat assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best cat/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The cat sequence used in this annotation is from\
the Dec. 2008 (NHGRI/GTB V17e/felCat4) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the cat/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single cat chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) Alignment Net\
parent chainNetFelCat4Viewnet\
shortLabel Cat Net\
subGroups view=net\
track netFelCat4\
type netAlign felCat4 chainFelCat4\

netMonDom5	Opossum Net	netAlign monDom5 chainMonDom5	Opossum (Oct. 2006 (Broad/monDom5)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of opossum (Oct. 2006 (Broad/monDom5)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
opossum and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
opossum assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best opossum/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The opossum sequence used in this annotation is from\
the Oct. 2006 (Broad/monDom5) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the opossum/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single opossum chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Opossum (Oct. 2006 (Broad/monDom5)) Alignment Net\
parent chainNetMonDom5Viewnet\
shortLabel Opossum Net\
subGroups view=net\
track netMonDom5\
type netAlign monDom5 chainMonDom5\

netPetMar1	Lamprey Net	netAlign petMar1 chainPetMar1	Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
lamprey and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
lamprey assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best lamprey/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The lamprey sequence used in this annotation is from\
the Mar. 2007 (WUGSC 3.0/petMar1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the lamprey/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single lamprey chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) Alignment Net\
parent chainNetPetMar1Viewnet\
shortLabel Lamprey Net\
subGroups view=net\
track netPetMar1\
type netAlign petMar1 chainPetMar1\

netHg19	Human Net	netAlign hg19 chainHg19	Human (Feb. 2009 (GRCh37/hg19)) Alignment net	2	2	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
human and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
human assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best human/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The human sequence used in this annotation is from\
the Feb. 2009 (GRCh37/hg19) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the human/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single human chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Human (Feb. 2009 (GRCh37/hg19)) Alignment net\
parent chainNetHg19Viewnet\
shortLabel Human Net\
subGroups view=net\
track netHg19\
type netAlign hg19 chainHg19\

netOrnAna1	Platypus Net	netAlign ornAna1 chainOrnAna1	Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
platypus and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
platypus assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best platypus/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The platypus sequence used in this annotation is from\
the Mar. 2007 (WUGSC 5.0.1/ornAna1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the platypus/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single platypus chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) Alignment Net\
parent chainNetOrnAna1Viewnet\
shortLabel Platypus Net\
subGroups view=net\
track netOrnAna1\
type netAlign ornAna1 chainOrnAna1\

netFr2	Fugu Net	netAlign fr2 chainFr2	Fugu (Oct. 2004 (JGI 4.0/fr2)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of fugu (Oct. 2004 (JGI 4.0/fr2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
fugu and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
fugu assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best fugu/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The fugu sequence used in this annotation is from\
the Oct. 2004 (JGI 4.0/fr2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the fugu/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single fugu chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Fugu (Oct. 2004 (JGI 4.0/fr2)) Alignment Net\
parent chainNetFr2Viewnet\
shortLabel Fugu Net\
subGroups view=net\
track netFr2\
type netAlign fr2 chainFr2\

netCalJac3	Marmoset Net	netAlign calJac3 chainCalJac3	Marmoset (March 2009 (WUGSC 3.2/calJac3)) Alignment net	2	2	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of marmoset (March 2009 (WUGSC 3.2/calJac3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
marmoset and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
marmoset assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best marmoset/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The marmoset sequence used in this annotation is from\
the March 2009 (WUGSC 3.2/calJac3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the marmoset/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single marmoset chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Marmoset (March 2009 (WUGSC 3.2/calJac3)) Alignment net\
parent chainNetCalJac3Viewnet\
shortLabel Marmoset Net\
subGroups view=net\
track netCalJac3\
type netAlign calJac3 chainCalJac3\

netOryCun2	Rabbit Net	netAlign oryCun2 chainOryCun2	Rabbit (Apr. 2009 (Broad/oryCun2)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of rabbit (Apr. 2009 (Broad/oryCun2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
rabbit and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
rabbit assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best rabbit/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The rabbit sequence used in this annotation is from\
the Apr. 2009 (Broad/oryCun2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the rabbit/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single rabbit chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Rabbit (Apr. 2009 (Broad/oryCun2)) Alignment Net\
parent chainNetOryCun2Viewnet\
shortLabel Rabbit Net\
subGroups view=net\
track netOryCun2\
type netAlign oryCun2 chainOryCun2\

netTetNig2	Tetraodon Net	netAlign tetNig2 chainTetNig2	Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
tetraodon and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
tetraodon assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best tetraodon/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The tetraodon sequence used in this annotation is from\
the Mar. 2007 (Genoscope 8.0/tetNig2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the tetraodon/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single tetraodon chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) Alignment Net\
parent chainNetTetNig2Viewnet\
shortLabel Tetraodon Net\
subGroups view=net\
track netTetNig2\
type netAlign tetNig2 chainTetNig2\

netPanTro3	Chimp Net	netAlign panTro3 chainPanTro3	Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) Alignment net	2	2	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
chimp and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
chimp assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best chimp/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The chimp sequence used in this annotation is from\
the Oct. 2010 (CGSC 2.1.3/panTro3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the chimp/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single chimp chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) Alignment net\
parent chainNetPanTro3Viewnet\
shortLabel Chimp Net\
subGroups view=net\
track netPanTro3\
type netAlign panTro3 chainPanTro3\

netBosTau6	Cow Net	netAlign bosTau6 chainBosTau6	Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
cow and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
cow assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best cow/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The cow sequence used in this annotation is from\
the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the cow/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single cow chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) Alignment Net\
parent chainNetBosTau6Viewnet\
shortLabel Cow Net\
subGroups view=net\
track netBosTau6\
type netAlign bosTau6 chainBosTau6\

netSusScr2	Pig Net	netAlign susScr2 chainSusScr2	Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) Alignment Net	2	2	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
pig and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
pig assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best pig/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The pig sequence used in this annotation is from\
the Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the pig/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single pig chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) Alignment Net\
parent chainNetSusScr2Viewnet\
shortLabel Pig Net\
subGroups view=net\
track netSusScr2\
type netAlign susScr2 chainSusScr2\

netPonAbe2	Orangutan Net	netAlign ponAbe2 chainPonAbe2	Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Alignment net	2	2	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
orangutan and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
orangutan assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best orangutan/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The orangutan sequence used in this annotation is from\
the July 2007 (WUGSC 2.0.2/ponAbe2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the orangutan/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single orangutan chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	0	html chainNet\
longLabel Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) Alignment net\
parent chainNetPonAbe2Viewnet\
shortLabel Orangutan Net\
subGroups view=net\
track netPonAbe2\
type netAlign ponAbe2 chainPonAbe2\

wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hRawRep1	10T1/2 Fibc Raw	bigWig 0.050000 719565.000000	10T1/2 Fibrocyte 60 h RNA-seq Raw Signal from ENCODE/Caltech	2	2	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel 10T1/2 Fibrocyte 60 h RNA-seq Raw Signal from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewRawSignal\
shortLabel 10T1/2 Fibc Raw\
subGroups view=RawSignal cellType=cell10T12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=E2P60H rep=rep1\
track wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hRawRep1\
type bigWig 0.050000 719565.000000\

wgEncodeUwDgf3134RiiiMImmortalPkRep1	3134 Immt P	narrowPeak	3134 Immortal RIII DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	2	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel 3134 Immortal RIII DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel 3134 Immt P\
subGroups view=Peaks age=IMMORTAL cellType=Cel3134 strain=RIII treatment=NONE rep=rep1\
track wgEncodeUwDgf3134RiiiMImmortalPkRep1\
type narrowPeak\

wgEncodeUwDnase3134RiiiMImmortalPkRep1	3134 P 1	narrowPeak	3134 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	2	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel 3134 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks\
shortLabel 3134 P 1\
subGroups view=Peaks age=IMMORTAL cellType=A13134 sex=M strain=RIII rep=rep1 treatment=zNONE\
track wgEncodeUwDnase3134RiiiMImmortalPkRep1\
type narrowPeak\

wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep2	A20 A 2	bam	A20 Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW	0	2	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel A20 Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel A20 A 2\
subGroups view=Alignments age=IMMORTAL cellType=A20 localization=CELL rnaExtract=POLYA sex=M strain=BALBCANN rep=rep2\
track wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannAlnRep2\
type bam\

wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep1	Adrenal - 1	bigWig 1.000000 461984.000000	Adrenal A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	2	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Adrenal A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Adrenal - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=ADRENAL rep=rep1\
track wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep1\
type bigWig 1.000000 461984.000000\

agilentCgh4x180k	Ag CGH 4x180K	bed 4 .	Agilent SurePrint G3 Mouse CGH Microarray 4x180K AMADID 027411	0	2	255	128	0	255	191	127	0	0	0				varRep	1	color 255,128,0\
longLabel Agilent SurePrint G3 Mouse CGH Microarray 4x180K AMADID 027411\
nextItemButton off\
noScoreFilter .\
parent genotypeArrays\
priority 2\
shortLabel Ag CGH 4x180K\
track agilentCgh4x180k\
type bed 4 .\

wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep2	BAT 24wk Al 2	bam	Brown Adipose Tissue Adult 24 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	2	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Brown Adipose Tissue Adult 24 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel BAT 24wk Al 2\
subGroups view=Alignments age=ADULT24WKS cellType=BAT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6AlnRep2\
type bam\

wgEncodeLicrHistoneBcellcd43nH3k27me3MAdlt8wC57bl6StdSig	BCD43- H3K27m3	bigWig 0.150000 41.919998	B-cell (CD43-) 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	2	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BCD43- H3K27m3\
subGroups view=Signal age=A1DLT8W factor=H3K27ME3 cellType=B0CELLCD43N control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBcellcd43nH3k27me3MAdlt8wC57bl6StdSig\
type bigWig 0.150000 41.919998\
viewLimits 0.2:2\

wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdSig	BM 8w CTCF	bigWig 0.150000 40.070000	Bone Marrow Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	2	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Bone Marrow Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel BM 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsBmarrowCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.150000 40.070000\
viewLimits 0.2:5\

wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xSigRep1	C2 CEBPB 60h 1	bigWig 0.047900 13241.905273	C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	2	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 CEBPB 60h 1\
subGroups view=Signal factor=CEBPB cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.047900 13241.905273\

wgEncodeCaltechHistC2c12Ab2621FCntrl50bPcr1xSigRep1	C2 H3K79me3 1	bigWig 0.065000 7717.262207	C2C12 H379me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	2	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H379me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 H3K79me3 1\
subGroups view=Signal factor=AB2621 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12Ab2621FCntrl50bPcr1xSigRep1\
type bigWig 0.065000 7717.262207\

wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41AlnRep1	CH12 A 1	bam	CH12 1x41 RNA-seq Alignments Rep 1 from ENCODE/PSU	0	2	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 1x41 RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel CH12 A 1\
subGroups view=Alignments age=IMMORTAL cellType=CH12 readType=R1X41 sex=F strain=s2A4B treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41AlnRep1\
type bam\

wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep2	CH12 Aln 2	bam	CH12 RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale	1	2	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale\
origAssembly mm9\
parent wgEncodeSydhRnaSeqViewAlignments\
shortLabel CH12 Aln 2\
subGroups view=Alignments cellType=CH12 readType=R2X101D rnaExtract=RIBOZEROG treatment=NONE rep=rep2\
track wgEncodeSydhRnaSeqCh12RibozerogR2x101dAlnRep2\
type bam\

wgEncodeSydhTfbsCh12Bhlhe40nb100IggrabSig	CH12 BHLHE40	bigWig 1.000000 125631.000000	CH12 BHLHE40 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	2	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 BHLHE40 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
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wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputSig	CH12 CTCF	bigWig 1.000000 226.000000	CH12 CTCF TFBS ChIP-seq Signal from ENCODE/PSU	2	2	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 CTCF TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
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track wgEncodePsuTfbsCh12CtcfFImmortal2a4bInputSig\
type bigWig 1.000000 226.000000\
viewLimits 1:100\

wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputSig	CH12 H3K4m1	bigWig 1.000000 479.000000	CH12 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	2	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel CH12 H3K4m1\
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track wgEncodePsuHistoneCh12H3k04me1FImmortal2a4bInputSig\
type bigWig 1.000000 479.000000\
viewLimits 2:250\

wgEncodeSydhHistCh12H3k4me3IggyaleSig	CH12 H3K4m3 Y	bigWig 1.000000 45491.000000	CH12 H3K4me3 IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	2	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K4me3 IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig\
shortLabel CH12 H3K4m3 Y\
subGroups view=Signal factor=H3K04ME3 cellType=CH12 control=IGGYale treatment=zNONE\
track wgEncodeSydhHistCh12H3k4me3IggyaleSig\
type bigWig 1.000000 45491.000000\

wgEncodeFsuRepliChipCh12FWaveSignalRep2	CH12 Ws 2	bigWig -1.740197 1.319845	CH12 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	2	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip\
shortLabel CH12 Ws 2\
subGroups view=WaveSignal cellType=CH12 sex=F treatment=NONE rep=rep2\
track wgEncodeFsuRepliChipCh12FWaveSignalRep2\
type bigWig -1.740197 1.319845\

wgEncodeCrgMapabilityAlign40mer	CRG Align 40	bigWig 0.00 1.00	Alignability of 40mers by GEM from ENCODE/CRG(Guigo)	0	2	120	0	0	187	127	127	0	0	0				map	0	color 120,0,0\
longLabel Alignability of 40mers by GEM from ENCODE/CRG(Guigo)\
parent wgEncodeMapability\
priority 2\
shortLabel CRG Align 40\
subGroups win=w040 lab=CRG\
track wgEncodeCrgMapabilityAlign40mer\

ensGene	Ensembl Genes	genePred ensPep	Ensembl Genes	3	2	150	0	0	202	127	127	0	0	0			<h2>Description</h2>\
\
<p>\
These gene predictions were generated by <a href="http://www.ensembl.org/index.html"\
target="_blank">Ensembl</a>.\
</p>\
\
<p>\
For more information on the different gene tracks, see our <a target=_blank \
href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>\
\
<h2>Methods</h2>\
\
<p>\
For a description of the methods used in Ensembl gene predictions, please refer to\
<a href="https://academic.oup.com/nar/article/30/1/38/1332872/The-Ensembl-genome-database-project"\
target="_blank">Hubbard <em>et al</em>. (2002)</a>, also listed in the References section below. \
</p>\
\
<h2>Data access</h2>\
<p>\
Ensembl Gene data can be explored interactively using the\
<a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> or the\
<a href="/cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>. \
For local downloads, the genePred format files for mm9 are available in our\
<a target="_blank" href="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/">\
downloads directory</a> as ensGene.txt.gz or in our\
<a target="_blank" href="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/genes">\
genes download directory</a> in GTF format.<br><br>\
For programmatic access, the data can be queried from the \
<a href="../goldenPath/help/api.html" target="_blank">REST API</a> or\
directly from our public MySQL\
servers. Instructions on this method are available on our\
<a target="_blank" href="/goldenPath/help/mysql.html">MySQL help page</a> and on\
<a target="_blank" href="http://genome.ucsc.edu/blog/tag/mysql/">our blog</a>.</p>\
\
<p>\
Previous versions of this track can be found on our <a href="http://hgdownload.soe.ucsc.edu/goldenPath/archive/mm9/ensGene">archive download server</a>.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
We would like to thank Ensembl for providing these gene annotations. For more information, please see\
<a href="https://uswest.ensembl.org/info/genome/genebuild/index.html"\
target=_blank>Ensembl&#39s genome annotation page.</a>\
</p> \
\
<h2>References</h2>\
\
<p>\
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J,\
Curwen V, Down T <em>et al</em>.\
<a href="https://academic.oup.com/nar/article/30/1/38/1332872/The-Ensembl-genome-database-project"\
target="_blank">The Ensembl genome database project</a>.\
<em>Nucleic Acids Res</em>. 2002 Jan 1;30(1):38-41.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11752248" target="_blank">11752248</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99161/" target="_blank">PMC99161</a>\
</p>\
	genes	1	color 150,0,0\
exonNumbers on\
group genes\
longLabel Ensembl Genes\
priority 2\
shortLabel Ensembl Genes\
track ensGene\
type genePred ensPep\
visibility pack\

wgEncodePsuDnaseG1eS129ME0SigRep1	G1E 1	bigWig 0.000000 9015.792969	G1E DNaseI HS Signal Rep 1 from ENCODE/PSU	2	2	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E DNaseI HS Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuDnaseViewSignal\
shortLabel G1E 1\
subGroups view=Signal age=E0 cellType=G1E sex=M strain=S129 treatment=aNONE rep=rep1\
track wgEncodePsuDnaseG1eS129ME0SigRep1\
type bigWig 0.000000 9015.792969\

phyloP30wayPlacental	Mammal Cons	wig -9.46 2.06	Placental Mammal Basewise Conservation by PhyloP	2	2	25	25	95	95	25	25	0	0	0				compGeno	0	altColor 95,25,25\
autoScale off\
color 25,25,95\
configurable on\
longLabel Placental Mammal Basewise Conservation by PhyloP\
maxHeightPixels 100:50:11\
noInherit on\
parent cons30wayViewphyloP on\
priority 2\
shortLabel Mammal Cons\
spanList 1\
subGroups view=phyloP clade=mammal\
track phyloP30wayPlacental\
type wig -9.46 2.06\
viewLimits -3.3:2.1\
windowingFunction mean\

refSeqComposite	NCBI RefSeq	genePred	RefSeq genes from NCBI	1	2	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
<p>\
The NCBI RefSeq Genes composite track shows mouse protein-coding and non-protein-coding\
genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use\
coordinates provided by RefSeq, except for the <em>UCSC RefSeq</em> track, which UCSC produces by\
realigning the RefSeq RNAs to the genome. This realignment may result in occasional differences\
between the annotation coordinates provided by UCSC and NCBI. For RNA-seq analysis, we advise\
using NCBI aligned tables like RefSeq All or RefSeq Curated. See the \
<a href="#methods">Methods</a> section for more details about how the different tracks were \
created. </p>\
<p>\
Please visit NCBI's <a href="https://www.ncbi.nlm.nih.gov/projects/RefSeq/update.cgi"\
target="_blank">Feedback for Gene and Reference Sequences (RefSeq)</a> page to make suggestions, \
submit additions and corrections, or ask for help concerning RefSeq records. </p>\
\
<p>\
For more information on the different gene tracks, see our <a target=_blank \
href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>\
\
<h2>Display Conventions and Configuration</h2>\
<p>\
This track is a composite track that contains differing data sets.\
To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to \
hide. <b>Note:</b> Not all subtracts are available on all assemblies. </p>\
\
The possible subtracks include:\
<dl>\
  <dt><em><strong>RefSeq aligned annotations and UCSC alignment of RefSeq annotations\
          </strong></em></dt>\
  <ul>\
    <li>\
    <em>RefSeq All</em> &ndash; all curated and predicted annotations provided by \
    RefSeq.</li>\
    <li>\
    <em>RefSeq Curated</em> &ndash; subset of <em>RefSeq All</em> that includes only those \
    annotations whose accessions begin with NM, NR, NP or YP. <small>(NP and YP are used only for\
    protein-coding genes on the mitochondrion; YP is used for human only.)</small> They were \
    manually curated, based on publications describing transcripts and manual reviews of \
    evidence which includes EST and full-length cDNA alignments, protein sequences, splice sites\
    and any other evidence available in databases or the scientific literature. The \
    resulting sequences can differ from the genome, they exist independently \
    from a particular human genome build, and so must be aligned to the genome to create a track.\
    The "RefSeq Curated" track is NCBI's mapping of these transcripts to the genome.\
    Another alignment track exists for these, the "UCSC RefSeq" track (see beloow).</li>\
    <li>\
    <em>RefSeq Predicted</em> &ndash; subset of RefSeq All that includes those annotations whose \
    accessions begin with XM or XR. They were predicted based on protein, cDNA, EST\
    and RNA-seq alignments to the genome assembly by the NCBI Gnomon prediction software.</li>\
    <li>\
    <em>RefSeq Other</em> &ndash; all other annotations produced by the RefSeq group that \
    do not fit the requirements for inclusion in the <em>RefSeq Curated</em> or the \
    <em>RefSeq Predicted</em> tracks. Examples are untranscribed pseudogenes or gene clusters, such as HOX or protocadherin alpha. They were manually curated from \
    publications or databases but are not typical transcribed genes.</li>\
    <li>\
    <em>RefSeq Alignments</em> &ndash; alignments of RefSeq RNAs to the mouse genome provided\
    by the RefSeq group, following the display conventions for\
<a href="../goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank">PSL tracks</a>.</li>\
   <li>\
   <em>RefSeq Diffs</em> &ndash; alignment differences between the mouse reference genome(s) \
   and RefSeq curated transcripts. <small>(Track not currently available for every assembly.)</small>\
   </li>\
   <li>\
    <em>UCSC RefSeq</em> &ndash; annotations generated from UCSC's realignment of RNAs with NM \
    and NR accessions to the mouse genome. This track was previously known as the &quot;RefSeq \
    Genes&quot; track.</li>\
   <li>\
   <em>RefSeq Select (subset, only on hg38)</em> &ndash; Subset of RefSeq Curated, transcripts marked as \
   part of the RefSeq Select dataset. \
   A single <em>Select</em> transcript is chosen as representative for each protein-coding gene. \
   See <a target="_blank" \
   href="https://www.ncbi.nlm.nih.gov/refseq/refseq_select/">NCBI RefSeq Select</a>. \
   </li>\
   <li>\
   <em>RefSeq HGMD (subset)</em> &ndash; Subset of RefSeq Curated, transcripts annotated by the Human\
   Gene Mutation Database. This track is only available on the human genomes hg19 and hg38.\
   It is the most restricted RefSeq subset, targeting clinical diagnostics.\
   </li>\
  </ul>\
</dl>\
\
<p>\
The <em>RefSeq All</em>, <em>RefSeq Curated</em>, <em>RefSeq Predicted</em>, and\
<em>UCSC RefSeq</em> tracks follow the display conventions for\
<a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay"\
target="_blank">gene prediction tracks</a>.\
The color shading indicates the level of review the RefSeq record has undergone:\
predicted (light), provisional (medium), or reviewed (dark), as defined by <a target=_blank href="https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_status_codes/?report=objectonly">RefSeq</a>. </p>\
\
<p>\
<table>\
  <thead>\
  <tr>\
    <th style="border-bottom: 2px solid #6678B1;">Color</th>\
    <th style="border-bottom: 2px solid #6678B1;">Level of review</th>\
  </tr>\
  </thead>\
  <tr>\
    <th bgcolor="#0C0C78"></th>\
    <th align="left">Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information.</th>\
  </tr>\
  <tr>\
    <th bgcolor="#5050A0"></th>\
    <th align="left">Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff.</th>\
  </tr>\
  <tr>\
    <th bgcolor="#8282D2"></th>\
    <th align="left">Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted.</th>\
  </tr>\
</table>\
</p>\
\
<p>\
The item labels and codon display properties for features within this track can be configured \
through the check-box controls at the top of the track description page. To adjust the settings \
for an individual subtrack, click the wrench icon next to the track name in the subtrack list .</p>\
<ul>   \
  <li>\
  <strong>Label:</strong> By default, items are labeled by gene name. Click the appropriate Label \
  option to display the accession name or OMIM identifier instead of the gene name, show all or a \
  subset of these labels including the gene name, OMIM identifier and accession names, or turn off \
  the label completely.</li>\
  <li>\
  <strong>Codon coloring:</strong> This track has an optional codon coloring feature that \
  allows users to quickly validate and compare gene predictions. To display codon colors, select the\
  <em>genomic codons</em> option from the <em>Color track by codons</em> pull-down menu. For more \
  information about this feature, go to the <a href="../goldenPath/help/hgCodonColoring.html" \
  target="_blank">Coloring Gene Predictions and Annotations by Codon</a> page.</li>\
</ul>\
\
<p>The <em>RefSeq Diffs</em> track contains five different types of inconsistency between the\
reference genome sequence and the RefSeq transcript sequences. The five types of differences are\
as follows:\
<ul>\
  <li>\
   <em>mismatch</em> &ndash; aligned but mismatching bases, plus HGVS g. \
       to show the genomic change required to match the transcript and HGVS c./n. \
       to show the transcript change required to match the genome.</li>\
  <li>\
   <em>short gap</em> &ndash; genomic gaps that are too small to be introns (arbitrary cutoff of\
\	 &lt; 45 bp), most likely insertions/deletion variants or errors, with HGVS g. and c./n. \
\	showing differences.</li>\
  <li>\
   <em>shift gap</em> &ndash; shortGap items whose placement could be shifted left and/or right on\
\	the genome due to repetitive sequence, with HGVS c./n. position range of ambiguous region \
\	in transcript. Here, thin and thick lines are used -- the thin line shows the span of the\
\	repetitive sequence, and the thick line shows the rightmost shifted gap.\
       </li>\
  <li>\
   <em>double gap</em> &ndash; genomic gaps that are long enough to be introns but that skip over \
\	transcript sequence (invisible in default setting), with HGVS c./n. deletion.</li>\
  <li>\
   <em>skipped</em> &ndash; sequence at the beginning or end of a transcript that is not aligned to\
       the genome\
       (invisible in default setting), with HGVS c./n. deletion</li>\
\
</ul>\
\
<small><b>HGVS Terminology </b>(Human Genome Variation Society):\
\
g. = genomic sequence ; c. = coding DNA sequence ; n. = non-coding RNA reference sequence.</small>\
</p>\
\
<p>\
When reporting HGVS with RefSeq sequences, to make sure that results from\
research articles can be mapped to the genome unambiguously, \
please specify the RefSeq annotation release displayed on the transcript's\
Genome Browser details page and also the RefSeq transcript ID with version\
(e.g. NM_012309.4 not NM_012309). \
</p>\
\
\
<a name="methods"></a>\
<h2>Methods</h2>\
<p>\
Tracks contained in the RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using \
data from the NCBI RefSeq project. Data files were downloaded from RefSeq in GFF file format and \
converted to the genePred and PSL table formats for display in the Genome Browser. Information about\
the NCBI annotation pipeline can be found \
<a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/" target="_blank">here</a>.</p>\
\
<p>The RefSeq Diffs track is generated by UCSC using NCBI's RefSeq RNA alignments.</p>\
<p>\
The UCSC RefSeq Genes track is constructed using the same methods as previous RefSeq Genes tracks.\
RefSeq RNAs were aligned against the mouse genome using BLAT. Those with an alignment of\
less than 15% were discarded. When a single RNA aligned in multiple places, the alignment\
having the highest base identity was identified. Only alignments having a base identity\
level within 0.1% of the best and at least 96% base identity with the genomic sequence were\
kept.</p>\
\
<h2>Data Access</h2>\
<p>\
The raw data for these tracks can be accessed in multiple ways. It can be explored interactively \
using the <a href="/goldenPath/help/api.html" target="_blank">REST API</a>,\
<a href="../cgi-bin/hgTables" target="_blank">Table Browser</a> or\
<a href="../cgi-bin/hgIntegrator"\
target="_blank">Data Integrator</a>. The tables can also be accessed programmatically through our\
<a href="../../goldenPath/help/mysql.html"\
target="_blank">public MySQL server</a> or downloaded from our\
<a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/"\
target="_blank">downloads server</a> for local processing. The previous track versions are available\
in the <a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/mm9/ncbiRefSeq/"\
target="_blank">archives</a> of our downloads server. You can also access any RefSeq table\
entries in JSON format through our <a href="http://genome.ucsc.edu/goldenPath/help/api.html">\
JSON API</a>.</p>\
<p>\
The data in the <em>RefSeq Other</em> and <em>RefSeq Diffs</em> tracks are organized in \
<a href="../../FAQ/FAQformat.html#format1.5" target="_blank">bigBed</a> file format; more\
information about accessing the information in this bigBed file can be found\
below. The other subtracks are associated with database tables as follows:</p>\
<dl>\
  <dt><a href="../../FAQ/FAQformat.html#format9" target="_blank">genePred</a> format:</dt>\
  <ul>\
    <li>RefSeq All - <tt>ncbiRefSeq</tt></li>\
    <li>RefSeq Curated - <tt>ncbiRefSeqCurated</tt></li>\
    <li>RefSeq Predicted - <tt>ncbiRefSeqPredicted</tt></li>\
    <li>UCSC RefSeq - <tt>refGene</tt></li>\
  </ul>\
  <dt><a href="../../FAQ/FAQformat.html#format2" target="_blank">PSL</a> format:</dt>\
  <ul>\	\
    <li>RefSeq Alignments - <tt>ncbiRefSeqPsl</tt></li>\
  </ul>\
</dl>\
<p>\
The first column of each of these tables is &quot;bin&quot;. This column is designed\
to speed up access for display in the Genome Browser, but can be safely ignored in downstream\
analysis. You can read more about the bin indexing system\
<a href="http://genomewiki.ucsc.edu/index.php/Bin_indexing_system" target="_blank">here</a>.</p>\
<p>\
The annotations in the <em>RefSeqOther</em> and <em>RefSeqDiffs</em> tracks are stored in bigBed \
files, which can be obtained from our downloads server here,\
<a href="http://hgdownload.soe.ucsc.edu/gbdb/mm9/ncbiRefSeq/ncbiRefSeqOther.bb"\
target="_blank"><tt>ncbiRefSeqOther.bb</tt></a> and \
<a href="http://hgdownload.soe.ucsc.edu/gbdb/mm9/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb" \
target="_blank"><tt>ncbiRefSeqDiffs.bb</tt></a>.\
Individual regions or the whole set of genome-wide annotations can be obtained using our tool\
<tt>bigBedToBed</tt> which can be compiled from the source code or downloaded as a precompiled\
binary for your system from the utilities directory linked below. For example, to extract only\
annotations in a given region, you could use the following command:</p>\
<p>\
<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/mm9/ncbiRefSeq/ncbiRefSeqOther.bb\
-chrom=chr16 -start=34990190 -end=36727467 stdout</tt></p>\
<p>\
You can download a GTF format version of the RefSeq All table from the \
<a href="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/genes/">GTF downloads directory</a>.\
The genePred format tracks can also be converted to GTF format using the\
<tt>genePredToGtf</tt> utility, available from the\
<a href="http://hgdownload.soe.ucsc.edu/admin/exe/"\
target="_blank">utilities directory</a> on the UCSC downloads \
server. The utility can be run from the command line like so:</p>\
<tt>genePredToGtf mm9 ncbiRefSeqPredicted ncbiRefSeqPredicted.gtf</tt>\
<p>\
Note that using genePredToGtf in this manner accesses our public MySQL server, and you therefore \
must set up your hg.conf as described on the MySQL page linked near the beginning of the Data Access\
section.</p>\
<p>\
A file containing the RNA sequences in <a href="http://genetics.bwh.harvard.edu/pph/FASTA.html" \
target="_blank">FASTA</a> format for all items in the <em>RefSeq All</em>, <em>RefSeq Curated</em>, \
and <em>RefSeq Predicted</em> tracks can be found on our downloads server\
<a href="http://hgdownload.soe.ucsc.edu/gbdb/mm9/ncbiRefSeq/seqNcbiRefSeq.rna.fa"\
target="_blank">here</a>.</p>\
<p>\
Please refer to our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome"\
target="_blank">mailing list archives</a> for questions.</p>\
\
<p>\
Previous versions of the ncbiRefSeq set of tracks can be found on our <a href="http://hgdownload.soe.ucsc.edu/goldenPath/archive/mm9/ncbiRefSeq">archive download server</a>.\
</p>\
\
<h2>Credits</h2>\
<p>\
This track was produced at UCSC from data generated by scientists worldwide and curated by the\
NCBI RefSeq project. </p>\
\
<h2>References</h2>\
<p>\
Kent WJ.\
<a href="https://genome.cshlp.org/content/12/4/656.full" target="_blank">BLAT - the BLAST-like \
alignment tool</a>. <em>Genome Res.</em> 2002 Apr;12(4):656-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a></p>\
<p>\
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J,\
Landrum MJ, McGarvey KM <em>et al</em>.\
<a href="https://academic.oup.com/nar/article/42/D1/D756/1051112/RefSeq-an-update-on-mammalian-\
reference-sequences" target="_blank">RefSeq: an update on mammalian reference sequences</a>.\
<em>Nucleic Acids Res</em>. 2014 Jan;42(Database issue):D756-63.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24259432" target="_blank">24259432</a>; PMC: \
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965018/" target="_blank">PMC3965018</a></p>\
<p>\
Pruitt KD, Tatusova T, Maglott DR.\
<a href="https://academic.oup.com/nar/article/33/suppl_1/D501/2505241/NCBI-Reference-Sequence-\
RefSeq-a-curated-non" target="_blank">\
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts \
and proteins</a>.\
<em>Nucleic Acids Res.</em> 2005 Jan 1;33(Database issue):D501-4.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15608248" target="_blank">15608248</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979/" target="_blank">PMC539979</a></p>\
	genes	1	allButtonPair on\
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dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="http://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="http://www.informatics.jax.org/marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$"\
dragAndDrop subTracks\
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visibility dense\

numtSAssembled	NumtS assembled	bed 12 .	Mouse NumtS assembled	0	2	0	60	120	127	157	187	1	0	0			<h2>Description and display conventions</h2>\
\
<p> <b>NumtS</b> (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear\
genomic sequences. The most credited hypothesis concerning their generation suggests that in presence\
of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach\
the nucleus and insert into chromosomes during break repair; although NumtS can also derive from\
duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing\
and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group\
chaired by M. Attimonelli (University of Bari, Italy) has produced the RMmsNumtS (Reference Mus musculus\
NumtS) compilation annotating 148 Mouse assembled NumtS. To allow the scientific community to access \
the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the\
group has designed the Mouse NumtS tracks described below. </p>\
\
<p>The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs)\
obtained by aligning the mitochondrial reference genome (NC_005089) with the mm9 assembly of the\
mouse genome.</p> \
\
<ol> \
\	<li><b>"NumtS (Nuclear mitochondrial Sequences)" Track</b> \
\	<p> The "NumtS\
mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear\
genome. The shading of the items reflect the similarity returned by BlastN, and the direction of\
the arrows is concordant with the strand of the alignment. For every item, a link pointing to the\
mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. </p>\
\	</li>\
\
\	<li><b>"NumtS assembled" Track</b> \
\	<p> The "NumtS assembled" track shows items obtained by\
assembling HSPs annotated in the "NumtS" track fulfilling the following conditions:</p>\
\
\	\	<ul>\
\	\	\	<li>The orientation of their alignments must be concordant.</li> \
\	\	\	<li>The distance between them must be less than 2 kb, on the mitochondrial genome as \
\	\	\	well as on the nuclear genome.</li> \
\	\	</ul> \
\	\	\
\	<p>Exceptions for the second condition arise when a long repetitive element is present between\
\	 two HSPs.</p></li>\
\
\	<li><b>"NumtS on mitochondrion" Track</b>\
\	<p>The "NumtS on mitochondrion" track shows the mapping\
of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned\
by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every\
item, a link pointing to the nuclear mapping is provided.</p></li>\
\
\	<li><b>"Mouse NumtS on mitochondrion SNP" Track</b> \
\	<p>The "Mouse NumtS SNP" shows the mapping of\
the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison\
with the mm9 assembly. No shading is here provided. For every item, a link pointing to the nuclear\
mapping is provided.</p></li>\
</ol>\
\
<h2>Methods</h2> \
\
<p>NumtS mappings were obtained by running Blast2seq (program: BlastN) between\
each chromosome of the Mouse Genome (mm9 assembly) and the mouse mitochondrial reference sequence (AC:\
NC_005089), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with\
spreadsheet interpolation and manual inspection. BED format is used for the first three annotation\
tracks, while for the last one the SAM/BAM format is preferred.</p>\
\
<h2>Credits</h2>\
\
<p>These data were provided by Francesco Maria Calabrese, Domenico Simone and\
Marcella Attimonelli from the Department of Biochemistry and Molecular Biology "Ernesto \
Quagliariello" (University of Bari, Italy). Manual inspection and format details are carried out \
by Francesco Maria Calabrese, Domenico Simone and Luana Raddi.</p>\
\
<h2>References</h2>\
\
<p>\
Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M.\
<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-267" target="_blank">\
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human\
NumtS</a>.\
<em>BMC Genomics</em>. 2008 Jun 3;9:267.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18522722" target="_blank">18522722</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447851" target="_blank">PMC2447851</a>\
</p>\
\
<p>\
Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M.\
<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-517" target="_blank">\
The reference human nuclear mitochondrial sequences compilation validated and implemented on the\
UCSC genome browser</a>.\
<em>BMC Genomics</em>. 2011 Oct 20;12:517.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22013967" target="_blank">22013967</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228558" target="_blank">PMC3228558</a>\
</p>\
\
\
	varRep	1	color 0,60,120\
html numtSeqMm9\
longLabel Mouse NumtS assembled\
parent numtSeq\
priority 2\
shortLabel NumtS assembled\
track numtSAssembled\
type bed 12 .\
useScore 1\

polyASeqSitesBrainRev	PolyA-Seq Brain	bigWig 0.840000 6263.609863	Poly(A)-tail sequencing of Brain from Merck (Rev strand)	2	2	0	0	0	127	127	127	0	0	0				rna	0	color 0,0,0\
longLabel Poly(A)-tail sequencing of Brain from Merck (Rev strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Brain\
subGroups view=Signal tissType=Brain strand=rev\
track polyASeqSitesBrainRev\
type bigWig 0.840000 6263.609863\

rmsk	RepeatMasker	rmsk	Repeating Elements by RepeatMasker	1	2	0	0	0	127	127	127	1	0	0			<h2>Description</h2>\
\
<p>\
This track was created by using Arian Smit's\
<a href="http://www.repeatmasker.org/" target="_blank">RepeatMasker</a>\
program, which screens DNA sequences\
for interspersed repeats and low complexity DNA sequences. The program\
outputs a detailed annotation of the repeats that are present in the\
query sequence (represented by this track), as well as a modified version\
of the query sequence in which all the annotated repeats have been masked\
(generally available on the\
<a href="http://hgdownload.soe.ucsc.edu/downloads.html"\
target=_blank>Downloads</a> page). RepeatMasker uses the\
<a href="https://www.girinst.org/repbase/update/index.html"\
target=_blank>Repbase Update</a> library of repeats from the\
<a href="https://www.girinst.org/" target=_blank>Genetic \
Information Research Institute</a> (GIRI).\
Repbase Update is described in Jurka (2000) in the References section below.\
Some newer assemblies have been made with Dfam, not Repbase. You can\
find the details for how we make our database data here in our &quot;makeDb/doc/&quot;\
<a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/tree/master/src/hg/makeDb/doc/"\
target="_blank">directory</a>.</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
In full display mode, this track displays up to ten different classes of repeats:\
<ul>\
<li>Short interspersed nuclear elements (SINE), which include ALUs</li>\
<li>Long interspersed nuclear elements (LINE)</li>\
<li>Long terminal repeat elements (LTR), which include retroposons</li>\
<li>DNA repeat elements (DNA)</li>\
<li>Simple repeats (micro-satellites)</li>\
<li>Low complexity repeats</li>\
<li>Satellite repeats</li>\
<li>RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)</li>\
<li>Other repeats, which includes class RC (Rolling Circle)</li>\
<li>Unknown</li>\
</ul>\
</p>\
\
<p>\
The level of color shading in the graphical display reflects the amount of\
base mismatch, base deletion, and base insertion associated with a repeat\
element. The higher the combined number of these, the lighter the shading.\
</p>\
\
<p>\
A &quot;?&quot; at the end of the &quot;Family&quot; or &quot;Class&quot; (for example, DNA?) signifies that\
the curator was unsure of the classification. At some point in the future,\
either the &quot;?&quot; will be removed or the classification will be changed.</p>\
\
<h2>Methods</h2>\
\
<p>\
Data are generated using the RepeatMasker <em>-s</em> flag. Additional flags\
may be used for certain organisms.  Repeats are soft-masked. Alignments may\
extend through repeats, but are not permitted to initiate in them.\
See the <a href="/FAQ/FAQdownloads#download16" target="_blank">FAQ</a> for more information.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and\
repeat libraries used to generate this track.\
</p>\
\
<h2>References</h2>\
\
<p>\
Smit AFA, Hubley R, Green P. <em>RepeatMasker Open-3.0</em>.\
<a href="http://www.repeatmasker.org" target="_blank">\
http://www.repeatmasker.org</a>. 1996-2010.\
</p>\
\
<p>\
Repbase Update is described in:\
</p>\
\
<p>\
Jurka J.\
<a href="https://www.sciencedirect.com/science/article/pii/S016895250002093X" target="_blank">\
Repbase Update: a database and an electronic journal of repetitive elements</a>.\
<em>Trends Genet</em>. 2000 Sep;16(9):418-420.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10973072" target="_blank">10973072</a>\
</p>\
\
<p>\
For a discussion of repeats in mammalian genomes, see:\
</p>\
\
<p>\
Smit AF.\
<a href="https://www.sciencedirect.com/science/article/pii/S0959437X99000313" target="_blank">\
Interspersed repeats and other mementos of transposable elements in mammalian genomes</a>.\
<em>Curr Opin Genet Dev</em>. 1999 Dec;9(6):657-63.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10607616" target="_blank">10607616</a>\
</p>\
\
<p>\
Smit AF.\
<a href="https://www.sciencedirect.com/science/article/pii/S0959437X9680030X" target="_blank">\
The origin of interspersed repeats in the human genome</a>.\
<em>Curr Opin Genet Dev</em>. 1996 Dec;6(6):743-8.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8994846" target="_blank">8994846</a>\
</p>\
	varRep	0	canPack off\
group varRep\
longLabel Repeating Elements by RepeatMasker\
maxWindowToDraw 10000000\
priority 2\
shortLabel RepeatMasker\
spectrum on\
track rmsk\
type rmsk\
visibility dense\

pubsBlat	Sequences	bed 12 +	Sequences in Articles: PubmedCentral and Elsevier	1	2	0	0	0	127	127	127	0	0	0				pub	1	configurable off\
configureByPopup off\
longLabel Sequences in Articles: PubmedCentral and Elsevier\
parent pubs on\
priority 2\
shortLabel Sequences\
track pubsBlat\
type bed 12 +\
visibility dense\

cpgIslandExtUnmasked	Unmasked CpG	bed 4 +	CpG Islands on All Sequence (Islands < 300 Bases are Light Green)	0	2	0	100	0	128	228	128	0	0	0			<h2>Description</h2>\
\
<p>CpG islands are associated with genes, particularly housekeeping\
genes, in vertebrates.  CpG islands are typically common near\
transcription start sites and may be associated with promoter\
regions.  Normally a C (cytosine) base followed immediately by a \
G (guanine) base (a CpG) is rare in\
vertebrate DNA because the Cs in such an arrangement tend to be\
methylated.  This methylation helps distinguish the newly synthesized\
DNA strand from the parent strand, which aids in the final stages of\
DNA proofreading after duplication.  However, over evolutionary time,\
methylated Cs tend to turn into Ts because of spontaneous\
deamination.  The result is that CpGs are relatively rare unless\
there is selective pressure to keep them or a region is not methylated\
for some other reason, perhaps having to do with the regulation of gene\
expression.  CpG islands are regions where CpGs are present at\
significantly higher levels than is typical for the genome as a whole.</p>\
\
<p>\
The unmasked version of the track displays potential CpG islands\
that exist in repeat regions and would otherwise not be visible\
in the repeat masked version.\
</p>\
\
<p>\
By default, only the masked version of the track is displayed.  To view the\
unmasked version, change the visibility settings in the track controls at\
the top of this page.\
</p>\
\
<h2>Methods</h2>\
\
<p>CpG islands were predicted by searching the sequence one base at a\
time, scoring each dinucleotide (+17 for CG and -1 for others) and\
identifying maximally scoring segments.  Each segment was then\
evaluated for the following criteria:\
\
<ul>\
\	<li>GC content of 50% or greater</li>\
\	<li>length greater than 200 bp</li>\
\	<li>ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the \
\	basis of the number of Gs and Cs in the segment</li>\
</ul>\
</p>\
<p>\
The entire genome sequence, masking areas included, was\
used for the construction of the  track <em>Unmasked CpG</em>.\
The track <em>CpG Islands</em> is constructed on the sequence after\
all masked sequence is removed.\
</p>\
\
<p>The CpG count is the number of CG dinucleotides in the island.  \
The Percentage CpG is the ratio of CpG nucleotide bases\
(twice the CpG count) to the length.  The ratio of observed to expected \
CpG is calculated according to the formula (cited in \
Gardiner-Garden <em>et al</em>. (1987)):\
\
<pre>    Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)</pre>\
\
where N = length of sequence.</p>\
<p>\
The calculation of the track data is performed by the following command sequence:\
<pre>\
twoBitToFa <em>assembly.2bit</em> stdout | maskOutFa stdin hard stdout \\\
  | cpg_lh /dev/stdin 2&gt; cpg_lh.err \\\
    |  awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2;  printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \\\
     | sort -k1,1 -k2,2n &gt; cpgIsland.bed\
</pre>\
The <em>unmasked</em> track data is constructed from\
<em>twoBitToFa -noMask</em> output for the <em>twoBitToFa</em> command.\
</p>\
\
<h2>Data access</h2>\
<p>\
CpG islands and its associated tables can be explored interactively using the\
<a href="../goldenPath/help/api.html" target="_blank">REST API</a>, the\
<a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> or the\
<a href="/cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>.\
All the tables can also be queried directly from our public MySQL\
servers, with more information available on our\
<a target="_blank" href="/goldenPath/help/mysql.html">help page</a> as well as on\
<a target="_blank" href="http://genome.ucsc.edu/blog/tag/mysql/">our blog</a>.</p>\
<p>\
The source for the <em>cpg_lh</em> program can be obtained from\
<a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/tree/master/src/utils/cpgIslandExt/" target=_blank>src/utils/cpgIslandExt/</a>.\
The <em>cpg_lh</em> program binary can be obtained from: <a href="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh" download="cpg_lh">http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh</a> (choose "save file")\
</p>\
\
<h2>Credits</h2>\
\
<p>This track was generated using a modification of a program developed by G. Miklem and L. Hillier \
(unpublished).</p>\
\
<h2>References</h2>\
\
<p>\
Gardiner-Garden M, Frommer M.\
<a href="https://www.sciencedirect.com/science/article/pii/0022283687906899" target="_blank">\
CpG islands in vertebrate genomes</a>.\
<em>J Mol Biol</em>. 1987 Jul 20;196(2):261-82.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/3656447" target="_blank">3656447</a>\
</p>\
	regulation	1	html cpgIslandSuper\
longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green)\
parent cpgIslandSuper hide\
priority 2\
shortLabel Unmasked CpG\
track cpgIslandExtUnmasked\

vegaPseudoGene	Vega Pseudogenes	genePred vegaPep	Vega Annotated Pseudogenes and Immunoglobulin Segments	0	2	30	130	210	142	192	232	0	0	21	chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY,	http://vega.sanger.ac.uk/Mus_musculus/transview?transcript=$$		genes	1	color 30,130,210\
longLabel Vega Annotated Pseudogenes and Immunoglobulin Segments\
parent vegaGeneComposite\
priority 2\
shortLabel Vega Pseudogenes\
track vegaPseudoGene\

wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hSigRep1	10T1/2 Fibc Sig	bigWig 1.000000 719564.000000	10T1/2 Fibrocyte 60 h RNA-seq Signal (Unique Reads) from ENCODE/Caltech	0	3	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel 10T1/2 Fibrocyte 60 h RNA-seq Signal (Unique Reads) from ENCODE/Caltech\
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track wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200E2p60hSigRep1\
type bigWig 1.000000 719564.000000\

wgEncodeUwDgf3134RiiiMImmortalRawRep1	3134 Immt R	bigWig 1.000000 340336.000000	3134 Immortal RIII DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	3	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
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subGroups view=RawSignal age=IMMORTAL cellType=Cel3134 strain=RIII treatment=NONE rep=rep1\
track wgEncodeUwDgf3134RiiiMImmortalRawRep1\
type bigWig 1.000000 340336.000000\

wgEncodeUwDnase3134RiiiMImmortalSigRep1	3134 S 1	bigWig 1.000000 53562.000000	3134 DNaseI HS Signal Rep 1 from ENCODE/UW	2	3	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel 3134 DNaseI HS Signal Rep 1 from ENCODE/UW\
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shortLabel 3134 S 1\
subGroups view=Signal age=IMMORTAL cellType=A13134 sex=M strain=RIII rep=rep1 treatment=zNONE\
track wgEncodeUwDnase3134RiiiMImmortalSigRep1\
type bigWig 1.000000 53562.000000\

wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep1	A20 MR 1	bigWig 1.000000 60314.000000	A20 Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	3	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
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track wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep1\
type bigWig 1.000000 60314.000000\

wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep1	Adrenal + 1	bigWig 1.000000 554318.000000	Adrenal A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	3	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Adrenal A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
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subGroups view=PlusRawSignal age=ADULT8WKS cellType=ADRENAL rep=rep1\
track wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep1\
type bigWig 1.000000 554318.000000\

agilentCgh244a	Ag CGH 1x244K	bed 6 .	Agilent SurePrint HD Mouse CGH Microarray 1x244K AMADID 014695	0	3	0	128	0	127	191	127	0	0	0				varRep	1	color 0,128,0\
exonArrows on\
longLabel Agilent SurePrint HD Mouse CGH Microarray 1x244K AMADID 014695\
nextItemButton off\
noScoreFilter .\
parent genotypeArrays\
priority 3\
shortLabel Ag CGH 1x244K\
track agilentCgh244a\
type bed 6 .\

wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6SigRep1	BAT 24wk Sg 1	bigWig 0.000000 65489.000000	Brown Adipose Tissue Adult 24 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	3	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
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type bigWig 0.000000 65489.000000\

wgEncodeLicrHistoneBcellcd43nH3k36me3MAdlt8wC57bl6StdPk	BCD43- H3K36m3	broadPeak	B-cell (CD43-) 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	3	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
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subGroups view=Peaks age=A1DLT8W factor=H3K36ME3 cellType=B0CELLCD43N control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBcellcd43nH3k36me3MAdlt8wC57bl6StdPk\
type broadPeak\

wgEncodeLicrTfbsBmarrowInputMAdult8wksC57bl6StdSig	BM 8w Input	bigWig 0.150000 34.869999	Bone Marrow Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	3	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Bone Marrow Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
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track wgEncodeLicrTfbsBmarrowInputMAdult8wksC57bl6StdSig\
type bigWig 0.150000 34.869999\

wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xPkRep2	C2 CEBPB 60h 2	narrowPeak	C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Peaks Rep 2 from ENCODE/Caltech	3	3	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
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type narrowPeak\

wgEncodeCaltechHistC2c12Ab32356FCntrl50bE2p60hPcr1xPkRep1	C2 H3K4me2 60h 1	narrowPeak	C2C12 H3K4me2 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	3	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K4me2 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
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subGroups view=Peaks factor=AB32356 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12Ab32356FCntrl50bE2p60hPcr1xPkRep1\
type narrowPeak\

wgEncodeSydhTfbsCh12Chd1nb10060411IggrabPk	CH12 CHD1 P	narrowPeak	CH12 CHD1 (NB100-60411) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	3	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
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wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputPk	CH12 H3K4m3	broadPeak	CH12 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	3	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
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shortLabel CH12 H3K4m3\
subGroups view=Peaks age=IMMORTAL factor=H3K04ME3 cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputPk\
type broadPeak\

wgEncodeSydhHistCh12InputIggyaleSig	CH12 Input Y	bigWig 1.000000 59055.000000	CH12 Input IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	3	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Input IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel CH12 Input Y\
subGroups view=Signal factor=zInputIGGYALE cellType=CH12 control=IGGYale treatment=zNONE\
track wgEncodeSydhHistCh12InputIggyaleSig\
type bigWig 1.000000 59055.000000\

wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputPk	CH12 PAX5	broadPeak	CH12 PAX5 TFBS ChIP-seq Peaks from ENCODE/PSU	3	3	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 PAX5 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel CH12 PAX5\
subGroups view=Peaks age=IMMORTAL factor=PAX5c cellType=CH12 control=INPUT treatment=aNONE rep=repP sex=F strain=s2A4B\
track wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputPk\
type broadPeak\

wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41SigRep2	CH12 S 2	bigWig 1.000000 54769.000000	CH12 1x41 RNA-seq Signal Rep 2 from ENCODE/PSU	2	3	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 1x41 RNA-seq Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal off\
shortLabel CH12 S 2\
subGroups view=Signal age=IMMORTAL cellType=CH12 readType=R1X41 sex=F strain=s2A4B treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41SigRep2\
type bigWig 1.000000 54769.000000\

wgEncodeCrgMapabilityAlign50mer	CRG Align 50	bigWig 0.00 1.00	Alignability of 50mers by GEM from ENCODE/CRG(Guigo)	0	3	120	0	0	187	127	127	0	0	0				map	0	color 120,0,0\
longLabel Alignability of 50mers by GEM from ENCODE/CRG(Guigo)\
parent wgEncodeMapability\
priority 3\
shortLabel CRG Align 50\
subGroups win=w050 lab=CRG\
track wgEncodeCrgMapabilityAlign50mer\

wgEncodeFsuRepliChipEpisc5MWaveSignalRep1	EpiSC-5 Ws 1	bigWig -2.590480 2.178855	EpiSC-5 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	3	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel EpiSC-5 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel EpiSC-5 Ws 1\
subGroups view=WaveSignal cellType=EPISC5 sex=M treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipEpisc5MWaveSignalRep1\
type bigWig -2.590480 2.178855\

wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep1	ES-E14 Aln 1	bam	ES-E14 RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale	1	3	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale\
origAssembly mm9\
parent wgEncodeSydhRnaSeqViewAlignments\
shortLabel ES-E14 Aln 1\
subGroups view=Alignments cellType=ESE14 readType=R2X101D rnaExtract=RIBOZEROG treatment=NONE rep=rep1\
track wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep1\
type bam\

wgEncodePsuDnaseG1eS129ME0PkRep2	G1E 2	narrowPeak	G1E DNaseI HS Peaks Rep 2 from ENCODE/PSU	3	3	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E DNaseI HS Peaks Rep 2 from ENCODE/PSU\
parent wgEncodePsuDnaseViewPeaks\
shortLabel G1E 2\
subGroups view=Peaks age=E0 cellType=G1E sex=M strain=S129 treatment=aNONE rep=rep2\
track wgEncodePsuDnaseG1eS129ME0PkRep2\
type narrowPeak\

blastHg18KG	Human Proteins	psl protein	Human Proteins Mapped by Chained tBLASTn	3	3	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track contains tBLASTn alignments of the peptides from the predicted and \
known genes identified in the hg18 UCSC Genes track.</P>\
\
<H2>Methods</H2>\
First, the predicted proteins from the human UCSC Genes track were aligned \
with the human genome using the Blat program to discover exon boundaries.  \
Next, the amino acid sequences that make up each exon were aligned with the \
mouse sequence using the tBLASTn program.\
Finally, the putative mouse exons were chained together using an \
organism-specific maximum gap size but no gap penalty. The single best exon \
chains extending over more than 60% of the query protein were included. Exon \
chains that extended over 60% of the query and matched at least 60% of the \
protein's amino acids were also included.</P>\
\
<H2>Credits</H2> \
<P>\
tBLASTn is part of the NCBI BLAST tool set. For more information on BLAST, see\
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. \
<A HREF="https://www.sciencedirect.com/science/article/pii/S0022283605803602"\
TARGET=_blank>Basic local alignment search tool</A>. \
<em>J Mol Biol.</em> 1990 Oct 5;215(3):403-410.</P>\
<P>\
<A HREF="https://genome.cshlp.org/content/12/4/656.abstract"\
TARGET=_blank>Blat</A> was written by Jim Kent. The remaining utilities \
used to produce this track were written by Jim Kent or Brian Raney.</P>\
	genes	1	blastRef hg18.blastKGRef04\
colorChromDefault off\
group genes\
longLabel Human Proteins Mapped by Chained tBLASTn\
pred hg18.blastKGPep04\
priority 3\
shortLabel Human Proteins\
track blastHg18KG\
type psl protein\
visibility pack\

numtSMitochondrion	NumtS on mitochon	bed 6 .	Mouse NumtS on mitochondrion	0	3	0	60	120	127	157	187	1	0	1	chrM,		<h2>Description and display conventions</h2>\
\
<p> <b>NumtS</b> (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear\
genomic sequences. The most credited hypothesis concerning their generation suggests that in presence\
of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach\
the nucleus and insert into chromosomes during break repair; although NumtS can also derive from\
duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing\
and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group\
chaired by M. Attimonelli (University of Bari, Italy) has produced the RMmsNumtS (Reference Mus musculus\
NumtS) compilation annotating 148 Mouse assembled NumtS. To allow the scientific community to access \
the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the\
group has designed the Mouse NumtS tracks described below. </p>\
\
<p>The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs)\
obtained by aligning the mitochondrial reference genome (NC_005089) with the mm9 assembly of the\
mouse genome.</p> \
\
<ol> \
\	<li><b>"NumtS (Nuclear mitochondrial Sequences)" Track</b> \
\	<p> The "NumtS\
mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear\
genome. The shading of the items reflect the similarity returned by BlastN, and the direction of\
the arrows is concordant with the strand of the alignment. For every item, a link pointing to the\
mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. </p>\
\	</li>\
\
\	<li><b>"NumtS assembled" Track</b> \
\	<p> The "NumtS assembled" track shows items obtained by\
assembling HSPs annotated in the "NumtS" track fulfilling the following conditions:</p>\
\
\	\	<ul>\
\	\	\	<li>The orientation of their alignments must be concordant.</li> \
\	\	\	<li>The distance between them must be less than 2 kb, on the mitochondrial genome as \
\	\	\	well as on the nuclear genome.</li> \
\	\	</ul> \
\	\	\
\	<p>Exceptions for the second condition arise when a long repetitive element is present between\
\	 two HSPs.</p></li>\
\
\	<li><b>"NumtS on mitochondrion" Track</b>\
\	<p>The "NumtS on mitochondrion" track shows the mapping\
of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned\
by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every\
item, a link pointing to the nuclear mapping is provided.</p></li>\
\
\	<li><b>"Mouse NumtS on mitochondrion SNP" Track</b> \
\	<p>The "Mouse NumtS SNP" shows the mapping of\
the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison\
with the mm9 assembly. No shading is here provided. For every item, a link pointing to the nuclear\
mapping is provided.</p></li>\
</ol>\
\
<h2>Methods</h2> \
\
<p>NumtS mappings were obtained by running Blast2seq (program: BlastN) between\
each chromosome of the Mouse Genome (mm9 assembly) and the mouse mitochondrial reference sequence (AC:\
NC_005089), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with\
spreadsheet interpolation and manual inspection. BED format is used for the first three annotation\
tracks, while for the last one the SAM/BAM format is preferred.</p>\
\
<h2>Credits</h2>\
\
<p>These data were provided by Francesco Maria Calabrese, Domenico Simone and\
Marcella Attimonelli from the Department of Biochemistry and Molecular Biology "Ernesto \
Quagliariello" (University of Bari, Italy). Manual inspection and format details are carried out \
by Francesco Maria Calabrese, Domenico Simone and Luana Raddi.</p>\
\
<h2>References</h2>\
\
<p>\
Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M.\
<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-267" target="_blank">\
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human\
NumtS</a>.\
<em>BMC Genomics</em>. 2008 Jun 3;9:267.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18522722" target="_blank">18522722</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447851" target="_blank">PMC2447851</a>\
</p>\
\
<p>\
Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M.\
<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-517" target="_blank">\
The reference human nuclear mitochondrial sequences compilation validated and implemented on the\
UCSC genome browser</a>.\
<em>BMC Genomics</em>. 2011 Oct 20;12:517.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22013967" target="_blank">22013967</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228558" target="_blank">PMC3228558</a>\
</p>\
\
\
	varRep	1	chromosomes chrM\
color 0,60,120\
html numtSeqMm9\
longLabel Mouse NumtS on mitochondrion\
parent numtSeq\
priority 3\
shortLabel NumtS on mitochon\
track numtSMitochondrion\
type bed 6 .\
useScore 1\

polyASeqSitesKidneyFwd	PolyA-Seq Kidney	bigWig 0.260000 81890.773438	Poly(A)-tail sequencing of Kidney from Merck (Fwd strand)	2	3	153	51	51	204	153	153	0	0	0				rna	0	color 153,51,51\
longLabel Poly(A)-tail sequencing of Kidney from Merck (Fwd strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Kidney\
subGroups view=Signal tissType=Kidney strand=fwd\
track polyASeqSitesKidneyFwd\
type bigWig 0.260000 81890.773438\

phyloP30wayAll	Vertebrate Cons	wig -10.12 5.04	Vertebrate Basewise Conservation by PhyloP	2	3	25	25	95	95	25	25	0	0	0				compGeno	0	altColor 95,25,25\
autoScale off\
color 25,25,95\
configurable on\
longLabel Vertebrate Basewise Conservation by PhyloP\
maxHeightPixels 100:50:11\
noInherit on\
parent cons30wayViewphyloP off\
priority 3\
shortLabel Vertebrate Cons\
spanList 1\
subGroups view=phyloP clade=vert\
track phyloP30wayAll\
type wig -10.12 5.04\
viewLimits -4:4\
windowingFunction mean\

wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200AlnRep1	10T1/2 Fibb Aln	bam	10T1/2 Fibroblast RNA-seq Alignments from ENCODE/Caltech	0	4	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel 10T1/2 Fibroblast RNA-seq Alignments from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewAlignments off\
shortLabel 10T1/2 Fibb Aln\
subGroups view=Alignments cellType=cell10T12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=NONE rep=rep1\
track wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200AlnRep1\
type bam\

wgEncodeUwDnase3134RiiiMImmortalHotspotsRep2	3134 H 2	broadPeak	3134 DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	4	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel 3134 DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel 3134 H 2\
subGroups view=Hotspots age=IMMORTAL cellType=A13134 sex=M strain=RIII rep=rep2 treatment=zNONE\
track wgEncodeUwDnase3134RiiiMImmortalHotspotsRep2\
type broadPeak\

wgEncodeUwDgf3134RiiiMImmortalSigRep1	3134 Immt S	bigWig 1.000000 134493.000000	3134 Immortal RIII DNaseI DGF Signal Rep 1 from ENCODE/UW	2	4	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel 3134 Immortal RIII DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel 3134 Immt S\
subGroups view=Signal age=IMMORTAL cellType=Cel3134 strain=RIII treatment=NONE rep=rep1\
track wgEncodeUwDgf3134RiiiMImmortalSigRep1\
type bigWig 1.000000 134493.000000\

wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep2	A20 MR 2	bigWig 1.000000 40085.000000	A20 Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	4	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel A20 MR 2\
subGroups view=MinusRawSignal age=IMMORTAL cellType=A20 localization=CELL rnaExtract=POLYA sex=M strain=BALBCANN rep=rep2\
track wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannMinusRawRep2\
type bigWig 1.000000 40085.000000\

wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep2V2	Adrenal Aln 2	bam	Adrenal A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	4	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Adrenal A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Adrenal Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=ADRENAL rep=rep2\
track wgEncodeCshlLongRnaSeqAdrenalAdult8wksAlnRep2V2\
type bam\

agilentCgh105a	Ag CGH 2x105K	bed 6 .	Agilent SurePrint HD Mouse CGH Microarray 2x105K AMADID 014699	0	4	255	128	0	255	191	127	0	0	0				varRep	1	color 255,128,0\
exonArrows on\
longLabel Agilent SurePrint HD Mouse CGH Microarray 2x105K AMADID 014699\
nextItemButton off\
noScoreFilter .\
parent genotypeArrays\
priority 4\
shortLabel Ag CGH 2x105K\
track agilentCgh105a\
type bed 6 .\

wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6SigRep2	BAT 24wk Sg 2	bigWig 0.000000 65433.000000	Brown Adipose Tissue Adult 24 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	4	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Brown Adipose Tissue Adult 24 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel BAT 24wk Sg 2\
subGroups view=Signal age=ADULT24WKS cellType=BAT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqBatCellPapMAdult24wksC57bl6SigRep2\
type bigWig 0.000000 65433.000000\

wgEncodeLicrHistoneBcellcd43nH3k36me3MAdlt8wC57bl6StdSig	BCD43- H3K36m3	bigWig 0.140000 32.970001	B-cell (CD43-) 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	4	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BCD43- H3K36m3\
subGroups view=Signal age=A1DLT8W factor=H3K36ME3 cellType=B0CELLCD43N control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBcellcd43nH3k36me3MAdlt8wC57bl6StdSig\
type bigWig 0.140000 32.970001\
viewLimits 0.2:2\

wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdPk	BM 8w Pol2	broadPeak	Bone Marrow Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	4	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Bone Marrow Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel BM 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xSigRep2	C2 CEBPB 60h 2	bigWig 0.061800 10728.395508	C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Signal Rep 2 from ENCODE/Caltech	2	4	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 CEBPB Myocyte 60h TFBS ChIP-seq Signal Rep 2 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 CEBPB 60h 2\
subGroups view=Signal factor=CEBPB cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep2\
track wgEncodeCaltechTfbsC2c12CebpbFCntrl50bE2p60hPcr1xSigRep2\
type bigWig 0.061800 10728.395508\

wgEncodeCaltechHistC2c12Ab32356FCntrl50bE2p60hPcr1xSigRep1	C2 H3K4me2 60h 1	bigWig 0.056300 2937.138672	C2C12 H3K4me2 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	4	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3K4me2 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal\
shortLabel C2 H3K4me2 60h 1\
subGroups view=Signal factor=AB32356 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12Ab32356FCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.056300 2937.138672\

wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41AlnRep2	CH12 A 2	bam	CH12 1x41 RNA-seq Alignments Rep 2 from ENCODE/PSU	0	4	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 1x41 RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel CH12 A 2\
subGroups view=Alignments age=IMMORTAL cellType=CH12 readType=R1X41 sex=F strain=s2A4B treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqCh12FImmortal2a4bR1x41AlnRep2\
type bam\

wgEncodeSydhTfbsCh12Chd1nb10060411IggrabSig	CH12 CHD1 S	bigWig 1.000000 77123.000000	CH12 CHD1 (NB100-60411) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	4	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 CHD1 (NB100-60411) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 CHD1 S\
subGroups view=Signal factor=CHD1NB10060411 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Chd1nb10060411IggrabSig\
type bigWig 1.000000 77123.000000\

wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputSig	CH12 H3K4m3	bigWig 1.000000 480.000000	CH12 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	4	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel CH12 H3K4m3\
subGroups view=Signal age=IMMORTAL factor=H3K04ME3 cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12H3k04me3FImmortal2a4bInputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:500\

wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputSig	CH12 PAX5	bigWig 1.000000 106.000000	CH12 PAX5 TFBS ChIP-seq Signal from ENCODE/PSU	2	4	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 PAX5 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel CH12 PAX5\
subGroups view=Signal age=IMMORTAL factor=PAX5c cellType=CH12 control=INPUT treatment=aNONE rep=repP sex=F strain=s2A4B\
track wgEncodePsuTfbsCh12Pax5cFImmortal2a4bInputSig\
type bigWig 1.000000 106.000000\
viewLimits 2:100\

wgEncodeCrgMapabilityAlign75mer	CRG Align 75	bigWig 0.00 1.00	Alignability of 75mers by GEM from ENCODE/CRG(Guigo)	0	4	120	0	0	187	127	127	0	0	0				map	0	color 120,0,0\
longLabel Alignability of 75mers by GEM from ENCODE/CRG(Guigo)\
parent wgEncodeMapability\
priority 4\
shortLabel CRG Align 75\
subGroups win=w075 lab=CRG\
track wgEncodeCrgMapabilityAlign75mer\

wgEncodeFsuRepliChipEpisc5MWaveSignalRep2	EpiSC-5 Ws 2	bigWig -5.700624 3.277806	EpiSC-5 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	4	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel EpiSC-5 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel EpiSC-5 Ws 2\
subGroups view=WaveSignal cellType=EPISC5 sex=M treatment=NONE rep=rep2\
track wgEncodeFsuRepliChipEpisc5MWaveSignalRep2\
type bigWig -5.700624 3.277806\

wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep2	ES-E14 Aln 2	bam	ES-E14 RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale	1	4	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale\
origAssembly mm9\
parent wgEncodeSydhRnaSeqViewAlignments\
shortLabel ES-E14 Aln 2\
subGroups view=Alignments cellType=ESE14 readType=R2X101D rnaExtract=RIBOZEROG treatment=NONE rep=rep2\
track wgEncodeSydhRnaSeqEse14RibozerogR2x101dAlnRep2\
type bam\

wgEncodeSydhHistEse14H3k04me1StdPk	ES-E14 H3K4m1	narrowPeak	ES-E14 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	4	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks off\
shortLabel ES-E14 H3K4m1\
subGroups view=Peaks factor=H3K04ME1 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhHistEse14H3k04me1StdPk\
type narrowPeak\

wgEncodePsuDnaseG1eS129ME0SigRep2	G1E 2	bigWig 0.000000 174.242004	G1E DNaseI HS Signal Rep 2 from ENCODE/PSU	2	4	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E DNaseI HS Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuDnaseViewSignal\
shortLabel G1E 2\
subGroups view=Signal age=E0 cellType=G1E sex=M strain=S129 treatment=aNONE rep=rep2\
track wgEncodePsuDnaseG1eS129ME0SigRep2\
type bigWig 0.000000 174.242004\

bamMmsNumtSSorted	NumtS SNPs	bam	Mouse NumtS on mitochondrion SNPs	3	4	0	0	0	127	127	127	0	0	1	chrM,			varRep	1	aliQualRange 0:255\
bamColorMode strand\
bamGrayMode aliQual\
bamSkipPrintQualScore .\
baseColorDefault diffBases\
baseColorUseSequence lfExtra\
chromosomes chrM\
configurable on\
indelDoubleInsert on\
indelQueryInsert on\
longLabel Mouse NumtS on mitochondrion SNPs\
maxWindowToDraw 1000000\
noColorTag .\
pairEndsByName on\
parent numtSeq\
priority 4\
shortLabel NumtS SNPs\
showDiffBasesAllScales .\
showDiffBasesMaxZoom 100\
showNames on\
track bamMmsNumtSSorted\
type bam\
visibility pack\

polyASeqSitesKidneyRev	PolyA-Seq Kidney	bigWig 0.260000 51424.628906	Poly(A)-tail sequencing of Kidney from Merck (Rev strand)	2	4	0	0	0	127	127	127	0	0	0				rna	0	color 0,0,0\
longLabel Poly(A)-tail sequencing of Kidney from Merck (Rev strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Kidney\
subGroups view=Signal tissType=Kidney strand=rev\
track polyASeqSitesKidneyRev\
type bigWig 0.260000 51424.628906\

wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200RawRep1	10T1/2 Fibb Raw	bigWig 0.050000 2518819.000000	10T1/2 Fibroblast RNA-seq Raw Signal from ENCODE/Caltech	2	5	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel 10T1/2 Fibroblast RNA-seq Raw Signal from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewRawSignal\
shortLabel 10T1/2 Fibb Raw\
subGroups view=RawSignal cellType=cell10T12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=NONE rep=rep1\
track wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200RawRep1\
type bigWig 0.050000 2518819.000000\

wgEncodeUwDnase3134RiiiMImmortalPkRep2	3134 P 2	narrowPeak	3134 DNaseI HS Peaks Rep 2 from ENCODE/UW	3	5	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel 3134 DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel 3134 P 2\
subGroups view=Peaks age=IMMORTAL cellType=A13134 sex=M strain=RIII rep=rep2 treatment=zNONE\
track wgEncodeUwDnase3134RiiiMImmortalPkRep2\
type narrowPeak\

wgEncodeUwDgf416bB6d2f1jImmortalHotspotsRep1	416B Immt H	broadPeak	416B Immortal B6D2F1/J DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	5	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel 416B Immortal B6D2F1/J DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel 416B Immt H\
subGroups view=Hotspots age=IMMORTAL cellType=Cel416B strain=B6D2F1J treatment=NONE rep=rep1\
track wgEncodeUwDgf416bB6d2f1jImmortalHotspotsRep1\
type broadPeak\

wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep1	A20 PR 1	bigWig 1.000000 36016.000000	A20 Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	5	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel A20 PR 1\
subGroups view=PlusRawSignal age=IMMORTAL cellType=A20 localization=CELL rnaExtract=POLYA sex=M strain=BALBCANN rep=rep1\
track wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep1\
type bigWig 1.000000 36016.000000\

wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep2	Adrenal - 2	bigWig 1.000000 547818.000000	Adrenal A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	5	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Adrenal A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Adrenal - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=ADRENAL rep=rep2\
track wgEncodeCshlLongRnaSeqAdrenalAdult8wksMinusRawRep2\
type bigWig 1.000000 547818.000000\

wgEncodeLicrHistoneBcellcd43nInputMAdult8wksC57bl6StdSig	BCD43- Input	bigWig 0.140000 36.529999	B-cell (CD43-) 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	5	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BCD43- Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=B0CELLCD43N control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBcellcd43nInputMAdult8wksC57bl6StdSig\
type bigWig 0.140000 36.529999\
viewLimits 0.2:5\

wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdSig	BM 8w Pol2	bigWig 0.120000 46.389999	Bone Marrow Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	5	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Bone Marrow Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel BM 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsBmarrowPol2MAdult8wksC57bl6StdSig\
type bigWig 0.120000 46.389999\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep1	BM 8wk Al 1	bam	Bone Marrow Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	5	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Bone Marrow Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel BM 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=BMARROW localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeCaltechTfbsC2c12CebpbFCntrl50bPcr1xPkRep1	C2 CEBPB 1	narrowPeak	C2C12 CEBPB Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	5	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 CEBPB Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 CEBPB 1\
subGroups view=Peaks factor=CEBPB cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12CebpbFCntrl50bPcr1xPkRep1\
type narrowPeak\

wgEncodeCaltechHistC2c12Ab3594FCntrl50bE2p60hPcr1xPkRep1	C2 H3K79me2 60h 1	narrowPeak	C2C12 H3K79me2 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	5	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K79me2 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks off\
shortLabel C2 H3K79me2 60h 1\
subGroups view=Peaks factor=AB3594 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12Ab3594FCntrl50bE2p60hPcr1xPkRep1\
type narrowPeak\

wgEncodeSydhTfbsCh12Chd2ab68301IggrabPk	CH12 CHD2	narrowPeak	CH12 CHD2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	5	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 CHD2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 CHD2\
subGroups view=Peaks factor=CHD2AB68301 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Chd2ab68301IggrabPk\
type narrowPeak\

wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bInputPk	CH12 H3K9m3	broadPeak	CH12 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	5	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel CH12 H3K9m3\
subGroups view=Peaks age=IMMORTAL factor=H3K09ME3 cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bInputPk\
type broadPeak\

wgEncodePsuTfbsCh12InputFImmortal2a4bInputSig	CH12 Input	bigWig 1.000000 200.000000	CH12 Input TFBS ChIP-seq Signal from ENCODE/PSU	2	5	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Input TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel CH12 Input\
subGroups view=Signal age=IMMORTAL factor=zINPUT cellType=CH12 control=INPUT treatment=aNONE rep=repP sex=F strain=s2A4B\
track wgEncodePsuTfbsCh12InputFImmortal2a4bInputSig\
type bigWig 1.000000 200.000000\

wgEncodeCrgMapabilityAlign100mer	CRG Align 100	bigWig 0.00 1.00	Alignability of 100mers by GEM from ENCODE/CRG(Guigo)	0	5	120	0	0	187	127	127	0	0	0				map	0	color 120,0,0\
longLabel Alignability of 100mers by GEM from ENCODE/CRG(Guigo)\
parent wgEncodeMapability\
priority 5\
shortLabel CRG Align 100\
subGroups win=w100 lab=CRG\
track wgEncodeCrgMapabilityAlign100mer\

wgEncodeFsuRepliChipEpisc7FWaveSignalRep1	EpiSC-7 Ws 1	bigWig -7.988754 2.288202	EpiSC-7 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	5	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel EpiSC-7 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel EpiSC-7 Ws 1\
subGroups view=WaveSignal cellType=EPISC7 sex=F treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipEpisc7FWaveSignalRep1\
type bigWig -7.988754 2.288202\

wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dPlusRawRep1	Erythroblast P 1	bigWig 1.000000 23295684.000000	Erythroblast 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	5	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal\
shortLabel Erythroblast P 1\
subGroups view=PlusRawSignal age=E14HALF cellType=ERYTHROBL readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dPlusRawRep1\
type bigWig 1.000000 23295684.000000\

wgEncodeSydhHistEse14H3k04me1StdSig	ES-E14 H3K4m1	bigWig 1.000000 73084.000000	ES-E14 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	5	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel ES-E14 H3K4m1\
subGroups view=Signal factor=H3K04ME1 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhHistEse14H3k04me1StdSig\
type bigWig 1.000000 73084.000000\

wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep1	G1E-ER4 E2 24 1	narrowPeak	G1E-ER4 Estradiol 24hr DNaseI HS Peaks Rep 1 from ENCODE/PSU	3	5	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 24hr DNaseI HS Peaks Rep 1 from ENCODE/PSU\
parent wgEncodePsuDnaseViewPeaks\
shortLabel G1E-ER4 E2 24 1\
subGroups view=Peaks age=E0 cellType=G1EER4 sex=M strain=S129 treatment=DIFFD24H rep=rep1\
track wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep1\
type narrowPeak\

wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep1	MEL DMSO Aln 1	bam	MEL DMSO 2.0% RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale	1	5	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL DMSO 2.0% RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale\
origAssembly mm9\
parent wgEncodeSydhRnaSeqViewAlignments\
shortLabel MEL DMSO Aln 1\
subGroups view=Alignments cellType=MEL readType=R2X101D rnaExtract=RIBOZEROG treatment=DM2P5D rep=rep1\
track wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep1\
type bam\

xenoRefGene	Other RefSeq	genePred xenoRefPep xenoRefMrna	Non-Mouse RefSeq Genes	1	5	12	12	120	133	133	187	0	0	0			<H2>Description</H2>\
<P>\
This track shows known protein-coding and non-protein-coding genes \
for organisms other than mouse, taken from the NCBI RNA reference\
sequences collection (RefSeq). The data underlying this track are \
updated weekly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<P>\
This track follows the display conventions for \
<A HREF="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction \
tracks</A>.\
The color shading indicates the level of review the RefSeq record has \
undergone: predicted (light), provisional (medium), reviewed (dark).</P>\
<P>\
The item labels and display colors of features within this track can be\
configured through the controls at the top of the track description page. \
<UL>\
<LI><B>Label:</B> By default, items are labeled by gene name. Click the \
appropriate Label option to display the accession name instead of the gene\
name, show both the gene and accession names, or turn off the label \
completely.\
<LI><B>Codon coloring:</B> This track contains an optional codon coloring \
feature that allows users to quickly validate and compare gene predictions.\
To display codon colors, select the <em>genomic codons</em> option from the\
<em>Color track by codons</em> pull-down menu. Click \
<A HREF="../goldenPath/help/hgCodonColoring.html">here</A> for more \
information about this feature.\
<LI><B>Hide non-coding genes:</B> By default, both the protein-coding and\
non-protein-coding genes are displayed.  If you wish to see only the coding\
genes, click this box.\
</UL></P>\
\
<H2>Methods</H2>\
<P>\
The RNAs were aligned against the mouse genome using blat; those with an \
alignment of less than 15% were discarded. At least 40 bases must be aligned \
to DNA that is not repeat masked. When a single RNA aligned in multiple places, \
the alignment having the highest base identity was identified. Only alignments \
having a base identity level within 1.0% of the best and at least 35% base \
identity with the genomic sequence were kept. \
</P>\
\
<H2>Credits</H2>\
<P>\
This track was produced at UCSC from RNA sequence data\
generated by scientists worldwide and curated by the \
NCBI <A HREF="https://www.ncbi.nlm.nih.gov/refseq/" \
TARGET=_blank>RefSeq project</A>.  </P>\
\
<H2>References</H2>\
<p>\
Kent WJ.\
<a href="https://genome.cshlp.org/content/12/4/656.full" target="_blank">\
BLAT--the BLAST-like alignment tool</a>.\
<em>Genome Res</em>. 2002 Apr;12(4):656-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a>\
</p>\
	genes	1	color 12,12,120\
group genes\
longLabel Non-Mouse RefSeq Genes\
priority 5\
shortLabel Other RefSeq\
track xenoRefGene\
type genePred xenoRefPep xenoRefMrna\
visibility dense\

polyASeqSitesLiverFwd	PolyA-Seq Liver	bigWig 0.240000 53756.269531	Poly(A)-tail sequencing of Liver from Merck (Fwd strand)	2	5	153	51	51	204	153	153	0	0	0				rna	0	color 153,51,51\
longLabel Poly(A)-tail sequencing of Liver from Merck (Fwd strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Liver\
subGroups view=Signal tissType=Liver strand=fwd\
track polyASeqSitesLiverFwd\
type bigWig 0.240000 53756.269531\

wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200SigRep1	10T1/2 Fibb Sig	bigWig 1.000000 2072584.000000	10T1/2 Fibroblast RNA-seq Signal (Unique Reads) from ENCODE/Caltech	0	6	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel 10T1/2 Fibroblast RNA-seq Signal (Unique Reads) from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewSignal off\
shortLabel 10T1/2 Fibb Sig\
subGroups view=Signal cellType=cell10T12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=NONE rep=rep1\
track wgEncodeCaltechRnaSeq10t12C3hFR2x75Th131Il200SigRep1\
type bigWig 1.000000 2072584.000000\

wgEncodeUwDnase3134RiiiMImmortalSigRep2	3134 S 2	bigWig 1.000000 42784.000000	3134 DNaseI HS Signal Rep 2 from ENCODE/UW	2	6	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel 3134 DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel 3134 S 2\
subGroups view=Signal age=IMMORTAL cellType=A13134 sex=M strain=RIII rep=rep2 treatment=zNONE\
track wgEncodeUwDnase3134RiiiMImmortalSigRep2\
type bigWig 1.000000 42784.000000\

wgEncodeUwDgf416bB6d2f1jImmortalPkRep1	416B Immt P	narrowPeak	416B Immortal B6D2F1/J DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	6	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel 416B Immortal B6D2F1/J DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel 416B Immt P\
subGroups view=Peaks age=IMMORTAL cellType=Cel416B strain=B6D2F1J treatment=NONE rep=rep1\
track wgEncodeUwDgf416bB6d2f1jImmortalPkRep1\
type narrowPeak\

wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep2	A20 PR 2	bigWig 1.000000 39293.000000	A20 Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	6	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel A20 PR 2\
subGroups view=PlusRawSignal age=IMMORTAL cellType=A20 localization=CELL rnaExtract=POLYA sex=M strain=BALBCANN rep=rep2\
track wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannPlusRawRep2\
type bigWig 1.000000 39293.000000\

wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep2	Adrenal + 2	bigWig 1.000000 665516.000000	Adrenal A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	6	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Adrenal A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Adrenal + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=ADRENAL rep=rep2\
track wgEncodeCshlLongRnaSeqAdrenalAdult8wksPlusRawRep2\
type bigWig 1.000000 665516.000000\

wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep2	BM 8wk Al 2	bam	Bone Marrow Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	6	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Bone Marrow Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel BM 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=BMARROW localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdPk	BMDM 8w CTCF	broadPeak	BMDM Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	6	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel BMDM Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel BMDM 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrHistoneBmarrowH3k4me1MAdult8wksC57bl6StdPk	BoneMarrow H3K4m1	broadPeak	Bone Marrow 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	6	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Bone Marrow 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BoneMarrow H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBmarrowH3k4me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCaltechTfbsC2c12CebpbFCntrl50bPcr1xSigRep1	C2 CEBPB 1	bigWig 0.047900 18378.423828	C2C12 CEBPB Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	6	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 CEBPB Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 CEBPB 1\
subGroups view=Signal factor=CEBPB cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12CebpbFCntrl50bPcr1xSigRep1\
type bigWig 0.047900 18378.423828\

wgEncodeCaltechHistC2c12Ab3594FCntrl50bE2p60hPcr1xSigRep1	C2 H3K79me2 60h 1	bigWig 0.069700 5671.410645	C2C12 H3K79me2 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	6	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3K79me2 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 H3K79me2 60h 1\
subGroups view=Signal factor=AB3594 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12Ab3594FCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.069700 5671.410645\

wgEncodeSydhTfbsCh12Chd2ab68301IggrabSig	CH12 CHD2	bigWig 1.000000 169926.000000	CH12 CHD2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	6	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 CHD2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 CHD2\
subGroups view=Signal factor=CHD2AB68301 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Chd2ab68301IggrabSig\
type bigWig 1.000000 169926.000000\

wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bInputSig	CH12 H3K9m3	bigWig 1.000000 480.000000	CH12 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	6	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel CH12 H3K9m3\
subGroups view=Signal age=IMMORTAL factor=H3K09ME3 cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12H3k09me3FImmortal2a4bInputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:100\

wgEncodeFsuRepliChipEpisc7FWaveSignalRep2	EpiSC-7 Ws 2	bigWig -9.584117 1.922653	EpiSC-7 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	6	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel EpiSC-7 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel EpiSC-7 Ws 2\
subGroups view=WaveSignal cellType=EPISC7 sex=F treatment=NONE rep=rep2\
track wgEncodeFsuRepliChipEpisc7FWaveSignalRep2\
type bigWig -9.584117 1.922653\

wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputPk	Erythrobl GATA1	broadPeak	Erythroblast GATA1 TFBS ChIP-seq Peaks from ENCODE/PSU	3	6	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Erythroblast GATA1 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks\
shortLabel Erythrobl GATA1\
subGroups view=Peaks age=E14HALF factor=GATA1a cellType=ERYTHROBL control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputPk\
type broadPeak\

wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dMinusRawRep1	Erythroblast M 1	bigWig -26949678.000000 -1.000000	Erythroblast 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	6	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal\
shortLabel Erythroblast M 1\
subGroups view=MinusRawSignal age=E14HALF cellType=ERYTHROBL readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dMinusRawRep1\
type bigWig -26949678.000000 -1.000000\

wgEncodeSydhHistEse14H3k04me3StdPk	ES-E14 H3K4m3	narrowPeak	ES-E14 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	6	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks off\
shortLabel ES-E14 H3K4m3\
subGroups view=Peaks factor=H3K04ME3 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhHistEse14H3k04me3StdPk\
type narrowPeak\

wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep1	G1E-ER4 E2 24 1	bigWig 0.000000 6627.644531	G1E-ER4 Estradiol 24hr DNaseI HS Signal Rep 1 from ENCODE/PSU	2	6	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 24hr DNaseI HS Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuDnaseViewSignal\
shortLabel G1E-ER4 E2 24 1\
subGroups view=Signal age=E0 cellType=G1EER4 sex=M strain=S129 treatment=DIFFD24H rep=rep1\
track wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep1\
type bigWig 0.000000 6627.644531\

wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep2	MEL DMSO Aln 2	bam	MEL DMSO 2.0% RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale	1	6	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL DMSO 2.0% RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale\
origAssembly mm9\
parent wgEncodeSydhRnaSeqViewAlignments\
shortLabel MEL DMSO Aln 2\
subGroups view=Alignments cellType=MEL readType=R2X101D rnaExtract=RIBOZEROG treatment=DM2P5D rep=rep2\
track wgEncodeSydhRnaSeqMelDm2p5dRibozerogR2x101dAlnRep2\
type bam\

polyASeqSitesLiverRev	PolyA-Seq Liver	bigWig 0.240000 49296.449219	Poly(A)-tail sequencing of Liver from Merck (Rev strand)	2	6	0	0	0	127	127	127	0	0	0				rna	0	color 0,0,0\
longLabel Poly(A)-tail sequencing of Liver from Merck (Rev strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Liver\
subGroups view=Signal tissType=Liver strand=rev\
track polyASeqSitesLiverRev\
type bigWig 0.240000 49296.449219\

wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep1	416B H 1	broadPeak	416B DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	7	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel 416B DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel 416B H 1\
subGroups view=Hotspots age=IMMORTAL cellType=A1416B sex=M strain=B6D2F1J rep=rep1 treatment=zNONE\
track wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeUwDgf416bB6d2f1jImmortalRawRep1	416B Immt R	bigWig 1.000000 466076.000000	416B Immortal B6D2F1/J DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	7	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B Immortal B6D2F1/J DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel 416B Immt R\
subGroups view=RawSignal age=IMMORTAL cellType=Cel416B strain=B6D2F1J treatment=NONE rep=rep1\
track wgEncodeUwDgf416bB6d2f1jImmortalRawRep1\
type bigWig 1.000000 466076.000000\

wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep1	A20 S 1	bigWig 1.000000 60315.000000	A20 Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW	2	7	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel A20 S 1\
subGroups view=Signal age=IMMORTAL cellType=A20 localization=CELL rnaExtract=POLYA sex=M strain=BALBCANN rep=rep1\
track wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep1\
type bigWig 1.000000 60315.000000\

wgEncodeCshlLongRnaSeqAdrenalAdult8wksContigs	Adrenal C	bed 6 +	Adrenal A8 Long RNA-seq Contigs from ENCODE/CSHL	3	7	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Adrenal A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Adrenal C\
subGroups view=Contigs age=ADULT8WKS cellType=ADRENAL rep=repP\
track wgEncodeCshlLongRnaSeqAdrenalAdult8wksContigs\
type bed 6 +\

wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep1	BM 8wk Sg 1	bigWig 0.000000 65487.000000	Bone Marrow Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	7	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Bone Marrow Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel BM 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=BMARROW localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep1\
type bigWig 0.000000 65487.000000\

wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdSig	BMDM 8w CTCF	bigWig 0.160000 35.139999	BMDM Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	7	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel BMDM Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel BMDM 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrTfbsBmdmCtcfFAdult8wksC57bl6StdSig\
type bigWig 0.160000 35.139999\
viewLimits 0.2:5\

wgEncodeLicrHistoneBmarrowH3k4me1MAdult8wksC57bl6StdSig	BoneMarrow H3K4m1	bigWig 0.120000 20.459999	Bone Marrow 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	7	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Bone Marrow 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BoneMarrow H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBmarrowH3k4me1MAdult8wksC57bl6StdSig\
type bigWig 0.120000 20.459999\
viewLimits 0.2:3\

wgEncodeCaltechTfbsC2c12CtcfFCntrl32bPcr2xPkRep1	C2 CTCF 1	narrowPeak	C2C12 CTCF Myoblast ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	7	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 CTCF Myoblast ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 CTCF 1\
subGroups view=Peaks factor=CTCF cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12CtcfFCntrl32bPcr2xPkRep1\
type narrowPeak\

wgEncodeCaltechHistC2c12Ab3594FCntrl50bPcr1xPkRep1	C2 H3K79me2 1	narrowPeak	C2C12 H3K79me2 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	7	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K79me2 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks off\
shortLabel C2 H3K79me2 1\
subGroups view=Peaks factor=AB3594 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12Ab3594FCntrl50bPcr1xPkRep1\
type narrowPeak\

wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hAlnRep1	C2C12 Myoc Aln	bam	C2C12 Myocyte 60 h RNA-seq Alignments from ENCODE/Caltech	0	7	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Myocyte 60 h RNA-seq Alignments from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewAlignments off\
shortLabel C2C12 Myoc Aln\
subGroups view=Alignments cellType=cellC2C12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=E2P60H rep=rep1\
track wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hAlnRep1\
type bam\

wgEncodeSydhTfbsCh12Corestsc30189IggrabPk	CH12 COREST_s	narrowPeak	CH12 COREST (sc30189) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	7	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 COREST (sc30189) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 COREST_s\
subGroups view=Peaks factor=CORESTSC30189 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Corestsc30189IggrabPk\
type narrowPeak\

wgEncodePsuHistoneCh12H3k27me3FImmortal2a4bInputPk	CH12 H3K27m3	broadPeak	CH12 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	7	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel CH12 H3K27m3\
subGroups view=Peaks age=IMMORTAL factor=H3K27ME3 cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12H3k27me3FImmortal2a4bInputPk\
type broadPeak\

wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputSig	Erythrobl GATA1	bigWig 1.000000 248.000000	Erythroblast GATA1 TFBS ChIP-seq Signal from ENCODE/PSU	2	7	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast GATA1 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal\
shortLabel Erythrobl GATA1\
subGroups view=Signal age=E14HALF factor=GATA1a cellType=ERYTHROBL control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsErythroblGata1aBE14halfCd1InputSig\
type bigWig 1.000000 248.000000\
viewLimits 2:150\

wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dAlnRep1	Erythroblast A 1	bam	Erythroblast 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU	0	7	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Erythroblast 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel Erythroblast A 1\
subGroups view=Alignments age=E14HALF cellType=ERYTHROBL readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dAlnRep1\
type bam\

wgEncodeFsuRepliChipEs46cMDifff6dWaveSignalRep1	ES-46C NP Ws 1	bigWig -9.600121 2.012937	ES-46C NP 6 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	7	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-46C NP 6 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-46C NP Ws 1\
subGroups view=WaveSignal cellType=ES46C sex=M treatment=DIFFF6D rep=rep1\
track wgEncodeFsuRepliChipEs46cMDifff6dWaveSignalRep1\
type bigWig -9.600121 2.012937\

wgEncodeSydhHistEse14H3k04me3StdSig	ES-E14 H3K4m3	bigWig 1.000000 48136.000000	ES-E14 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	7	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel ES-E14 H3K4m3\
subGroups view=Signal factor=H3K04ME3 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhHistEse14H3k04me3StdSig\
type bigWig 1.000000 48136.000000\

wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep2	G1E-ER4 E2 24 2	narrowPeak	G1E-ER4 Estradiol 24hr DNaseI HS DNase-seq Peaks Rep 2 from ENCODE/PSU	3	7	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 24hr DNaseI HS DNase-seq Peaks Rep 2 from ENCODE/PSU\
parent wgEncodePsuDnaseViewPeaks\
shortLabel G1E-ER4 E2 24 2\
subGroups view=Peaks age=E0 cellType=G1EER4 sex=M strain=S129 treatment=DIFFD24H rep=rep2\
track wgEncodePsuDnaseG1eer4S129ME0Diffd24hPkRep2\
type narrowPeak\

wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep1	MEL Aln 1	bam	MEL RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale	1	7	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL RNA-seq Alignments Rep 1 from ENCODE/Stanford/Yale\
origAssembly mm9\
parent wgEncodeSydhRnaSeqViewAlignments\
shortLabel MEL Aln 1\
subGroups view=Alignments cellType=MEL readType=R2X101D rnaExtract=RIBOZEROG treatment=NONE rep=rep1\
track wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep1\
type bam\

polyASeqSitesMuscleFwd	PolyA-Seq Muscle	bigWig 0.180000 142298.031250	Poly(A)-tail sequencing of Muscle from Merck (Fwd strand)	2	7	153	51	51	204	153	153	0	0	0				rna	0	color 153,51,51\
longLabel Poly(A)-tail sequencing of Muscle from Merck (Fwd strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Muscle\
subGroups view=Signal tissType=Muscle strand=fwd\
track polyASeqSitesMuscleFwd\
type bigWig 0.180000 142298.031250\

wgEncodeUwDgf416bB6d2f1jImmortalSigRep1	416B Immt S	bigWig 1.000000 137025.000000	416B Immortal B6D2F1/J DNaseI DGF Signal Rep 1 from ENCODE/UW	2	8	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B Immortal B6D2F1/J DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel 416B Immt S\
subGroups view=Signal age=IMMORTAL cellType=Cel416B strain=B6D2F1J treatment=NONE rep=rep1\
track wgEncodeUwDgf416bB6d2f1jImmortalSigRep1\
type bigWig 1.000000 137025.000000\

wgEncodeUwDnase416bC57bl6MAdult8wksPkRep1	416B P 1	narrowPeak	416B DNaseI HS Peaks Rep 1 from ENCODE/UW	3	8	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel 416B DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel 416B P 1\
subGroups view=Peaks age=IMMORTAL cellType=A1416B sex=M strain=B6D2F1J rep=rep1 treatment=zNONE\
track wgEncodeUwDnase416bC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep2	A20 S 2	bigWig 1.000000 40090.000000	A20 Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW	2	8	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel A20 S 2\
subGroups view=Signal age=IMMORTAL cellType=A20 localization=CELL rnaExtract=POLYA sex=M strain=BALBCANN rep=rep2\
track wgEncodeUwRnaSeqA20CellPolyaMImmortalBalbcannSigRep2\
type bigWig 1.000000 40090.000000\

wgEncodeCshlLongRnaSeqAdrenalAdult8wksJunctions	Adrenal J	bed 6 +	Adrenal A8 Long RNA-seq Junctions from ENCODE/CSHL	0	8	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Adrenal A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Adrenal J\
subGroups view=SJunctions age=ADULT8WKS cellType=ADRENAL rep=repP\
track wgEncodeCshlLongRnaSeqAdrenalAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep2	BM 8wk Sg 2	bigWig 0.000000 65510.000000	Bone Marrow Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	8	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Bone Marrow Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel BM 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=BMARROW localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqBmarrowCellPapMAdult8wksC57bl6SigRep2\
type bigWig 0.000000 65510.000000\

wgEncodeLicrTfbsBmdmInputFAdult8wksC57bl6StdSig	BMDM 8w Input	bigWig 0.140000 48.919998	BMDM Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	8	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel BMDM Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel BMDM 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrTfbsBmdmInputFAdult8wksC57bl6StdSig\
type bigWig 0.140000 48.919998\

wgEncodeLicrHistoneBmarrowH3k4me3MAdult8wksC57bl6StdPk	BoneMarrow H3K4m3	broadPeak	Bone Marrow 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	8	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Bone Marrow 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BoneMarrow H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBmarrowH3k4me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCaltechTfbsC2c12CtcfFCntrl32bPcr2xSigRep1	C2 CTCF 1	bigWig 0.111000 885.506409	C2C12 CTCF Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	8	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 CTCF Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 CTCF 1\
subGroups view=Signal factor=CTCF cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12CtcfFCntrl32bPcr2xSigRep1\
type bigWig 0.111000 885.506409\

wgEncodeCaltechHistC2c12Ab3594FCntrl50bPcr1xSigRep1	C2 H3K79me2 1	bigWig 0.047300 4599.046875	C2C12 H3K79me2 Myoblast Histome Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	8	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3K79me2 Myoblast Histome Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 H3K79me2 1\
subGroups view=Signal factor=AB3594 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12Ab3594FCntrl50bPcr1xSigRep1\
type bigWig 0.047300 4599.046875\

wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hRawRep1	C2C12 Myoc Raw	bigWig 0.050000 513161.000000	C2C12 Myocyte 60 h RNA-seq Raw Signal from ENCODE/Caltech	2	8	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Myocyte 60 h RNA-seq Raw Signal from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewRawSignal\
shortLabel C2C12 Myoc Raw\
subGroups view=RawSignal cellType=cellC2C12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=E2P60H rep=rep1\
track wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hRawRep1\
type bigWig 0.050000 513161.000000\

wgEncodeSydhTfbsCh12Corestsc30189IggrabSig	CH12 COREST_s	bigWig 1.000000 160065.000000	CH12 COREST (sc30189) IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	8	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 COREST (sc30189) IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 COREST_s\
subGroups view=Signal factor=CORESTSC30189 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Corestsc30189IggrabSig\
type bigWig 1.000000 160065.000000\

wgEncodePsuHistoneCh12H3k27me3FImmortal2a4bInputSig	CH12 H3K27m3	bigWig 1.000000 480.000000	CH12 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	8	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel CH12 H3K27m3\
subGroups view=Signal age=IMMORTAL factor=H3K27ME3 cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12H3k27me3FImmortal2a4bInputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:200\

wgEncodePsuTfbsErythroblTal1BE14halfCd1InputPk	Erythrobl TAL1	broadPeak	Erythroblast TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU	3	8	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Erythroblast TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks\
shortLabel Erythrobl TAL1\
subGroups view=Peaks age=E14HALF factor=TAL1 cellType=ERYTHROBL control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsErythroblTal1BE14halfCd1InputPk\
type broadPeak\

wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dPlusRawRep2	Erythroblast P 2	bigWig 1.000000 23344592.000000	Erythroblast 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	8	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel Erythroblast P 2\
subGroups view=PlusRawSignal age=E14HALF cellType=ERYTHROBL readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dPlusRawRep2\
type bigWig 1.000000 23344592.000000\

wgEncodeFsuRepliChipEs46cMWaveSignalRep1	ES-46C Ws 1	bigWig -2.118093 5.296189	ES-46C Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	8	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-46C Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-46C Ws 1\
subGroups view=WaveSignal cellType=ES46C sex=M treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipEs46cMWaveSignalRep1\
type bigWig -2.118093 5.296189\

wgEncodeSydhHistEse14H3k09me3StdPk	ES-E14 H3K9m3	narrowPeak	ES-E14 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	8	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks off\
shortLabel ES-E14 H3K9m3\
subGroups view=Peaks factor=H3K09ME3 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhHistEse14H3k09me3StdPk\
type narrowPeak\

wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep2	G1E-ER4 E2 24 2	bigWig 0.000000 23.089300	G1E-ER4 Estradiol 24hr DNaseI HS DNase-seq Signal Rep 2 from ENCODE/PSU	2	8	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 24hr DNaseI HS DNase-seq Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuDnaseViewSignal\
shortLabel G1E-ER4 E2 24 2\
subGroups view=Signal age=E0 cellType=G1EER4 sex=M strain=S129 treatment=DIFFD24H rep=rep2\
track wgEncodePsuDnaseG1eer4S129ME0Diffd24hSigRep2\
type bigWig 0.000000 23.089300\

wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep2	MEL Aln 2	bam	MEL RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale	1	8	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL RNA-seq Alignments Rep 2 from ENCODE/Stanford/Yale\
origAssembly mm9\
parent wgEncodeSydhRnaSeqViewAlignments\
shortLabel MEL Aln 2\
subGroups view=Alignments cellType=MEL readType=R2X101D rnaExtract=RIBOZEROG treatment=NONE rep=rep2\
track wgEncodeSydhRnaSeqMelRibozerogR2x101dAlnRep2\
type bam\

polyASeqSitesMuscleRev	PolyA-Seq Muscle	bigWig 0.180000 21245.890625	Poly(A)-tail sequencing of Muscle from Merck (Rev strand)	2	8	0	0	0	127	127	127	0	0	0				rna	0	color 0,0,0\
longLabel Poly(A)-tail sequencing of Muscle from Merck (Rev strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Muscle\
subGroups view=Signal tissType=Muscle strand=rev\
track polyASeqSitesMuscleRev\
type bigWig 0.180000 21245.890625\

wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep1	416B A 1	bam	416B Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW	0	9	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel 416B Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel 416B A 1\
subGroups view=Alignments age=IMMORTAL cellType=ACel416B localization=CELL rnaExtract=POLYA sex=M strain=B6D2F1J rep=rep1\
track wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep1\
type bam\

wgEncodeUwDnase416bC57bl6MAdult8wksSigRep1	416B S 1	bigWig 1.000000 109673.000000	416B DNaseI HS Signal Rep 1 from ENCODE/UW	2	9	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel 416B S 1\
subGroups view=Signal age=IMMORTAL cellType=A1416B sex=M strain=B6D2F1J rep=rep1 treatment=zNONE\
track wgEncodeUwDnase416bC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 109673.000000\

wgEncodeUwDgfA20BalbcannMImmortalHotspotsRep1	A20 Immt H	broadPeak	A20 Immortal BALB/cAnN DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	9	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel A20 Immortal BALB/cAnN DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel A20 Immt H\
subGroups view=Hotspots age=IMMORTAL cellType=CelA20 strain=BALBCANN treatment=NONE rep=rep1\
track wgEncodeUwDgfA20BalbcannMImmortalHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep1	Bladder Aln 1	bam	Bladder A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	9	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Bladder A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Bladder Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=BLADDER rep=rep1\
track wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep1\
type bam\

wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdPk	BMDM 8w Pol2	broadPeak	BMDM Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	9	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel BMDM Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel BMDM 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1	BMDM 8wk Al 1	bam	BMDM Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	9	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel BMDM Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel BMDM 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=BMDM localization=CELL rnaExtract=PAP sex=F strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeLicrHistoneBmarrowH3k4me3MAdult8wksC57bl6StdSig	BoneMarrow H3K4m3	bigWig 0.120000 50.509998	Bone Marrow 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	9	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Bone Marrow 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BoneMarrow H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBmarrowH3k4me3MAdult8wksC57bl6StdSig\
type bigWig 0.120000 50.509998\
viewLimits 0.2:10\

wgEncodeCaltechTfbsC2c12E2f4FCntrl50bE2p60hPcr1xPkRep1	C2 E2F4 60h 1	narrowPeak	C2C12 E2F4 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	9	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 E2F4 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 E2F4 60h 1\
subGroups view=Peaks factor=E2F4 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12E2f4FCntrl50bE2p60hPcr1xPkRep1\
type narrowPeak\

wgEncodeCaltechHistC2c12H3ac06599FCntrl32bE2p24hPcr2xPkRep1	C2 H3ac 24h 1	narrowPeak	C2C12 H3ac Myocyte 24h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	9	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3ac Myocyte 24h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks off\
shortLabel C2 H3ac 24h 1\
subGroups view=Peaks factor=H3AC06599 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechHistC2c12H3ac06599FCntrl32bE2p24hPcr2xPkRep1\
type narrowPeak\

wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hSigRep1	C2C12 Myoc Sig	bigWig 1.000000 513148.000000	C2C12 Myocyte 60 h RNA-seq Signal (Unique Reads) from ENCODE/Caltech	0	9	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Myocyte 60 h RNA-seq Signal (Unique Reads) from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewSignal off\
shortLabel C2C12 Myoc Sig\
subGroups view=Signal cellType=cellC2C12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=E2P60H rep=rep1\
track wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200E2p60hSigRep1\
type bigWig 1.000000 513148.000000\

wgEncodeSydhTfbsCh12CtcfbIggrabPk	CH12 CTCF	narrowPeak	CH12 CTCF TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	9	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 CTCF TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks\
shortLabel CH12 CTCF\
subGroups view=Peaks factor=CTCFb cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12CtcfbIggrabPk\
type narrowPeak\

wgEncodePsuHistoneCh12H3k36me3FImmortal2a4bInputPk	CH12 H3K36m3	broadPeak	CH12 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	9	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel CH12 H3K36m3\
subGroups view=Peaks age=IMMORTAL factor=H3K36ME3 cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12H3k36me3FImmortal2a4bInputPk\
type broadPeak\

wgEncodePsuTfbsErythroblTal1BE14halfCd1InputSig	Erythrobl TAL1	bigWig 1.000000 268.000000	Erythroblast TAL1 TFBS ChIP-seq Signal from ENCODE/PSU	2	9	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast TAL1 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal\
shortLabel Erythrobl TAL1\
subGroups view=Signal age=E14HALF factor=TAL1 cellType=ERYTHROBL control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsErythroblTal1BE14halfCd1InputSig\
type bigWig 1.000000 268.000000\
viewLimits 2:250\

wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dMinusRawRep2	Erythroblast M 2	bigWig -21627596.000000 -1.000000	Erythroblast 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	9	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel Erythroblast M 2\
subGroups view=MinusRawSignal age=E14HALF cellType=ERYTHROBL readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dMinusRawRep2\
type bigWig -21627596.000000 -1.000000\

wgEncodeFsuRepliChipEsd3MDiffe3dWaveSignalRep1	ES-D3 EBM3 Ws 1	bigWig -9.098131 1.871574	ES-D3 EBM 3 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	9	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 EBM 3 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 EBM3 Ws 1\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=DIFFE3D rep=rep1\
track wgEncodeFsuRepliChipEsd3MDiffe3dWaveSignalRep1\
type bigWig -9.098131 1.871574\

wgEncodeSydhHistEse14H3k09me3StdSig	ES-E14 H3K9m3	bigWig 1.000000 222208.000000	ES-E14 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	9	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel ES-E14 H3K9m3\
subGroups view=Signal factor=H3K09ME3 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhHistEse14H3k09me3StdSig\
type bigWig 1.000000 222208.000000\

polyASeqSitesTestisFwd	PolyA-Seq Testis	bigWig 0.420000 18935.230469	Poly(A)-tail sequencing of Testis from Merck (Fwd strand)	2	9	153	51	51	204	153	153	0	0	0				rna	0	color 153,51,51\
longLabel Poly(A)-tail sequencing of Testis from Merck (Fwd strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Testis\
subGroups view=Signal tissType=Testis strand=fwd\
track polyASeqSitesTestisFwd\
type bigWig 0.420000 18935.230469\

wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep2	416B A 2	bam	416B Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW	0	10	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel 416B Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel 416B A 2\
subGroups view=Alignments age=IMMORTAL cellType=ACel416B localization=CELL rnaExtract=POLYA sex=M strain=B6D2F1J rep=rep2\
track wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jAlnRep2\
type bam\

wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep2	416B H 2	broadPeak	416B DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	10	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel 416B DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel 416B H 2\
subGroups view=Hotspots age=IMMORTAL cellType=A1416B sex=M strain=B6D2F1J rep=rep2 treatment=zNONE\
track wgEncodeUwDnase416bC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeUwDgfA20BalbcannMImmortalPkRep1	A20 Immt P	narrowPeak	A20 Immortal BALB/cAnN DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	10	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel A20 Immortal BALB/cAnN DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel A20 Immt P\
subGroups view=Peaks age=IMMORTAL cellType=CelA20 strain=BALBCANN treatment=NONE rep=rep1\
track wgEncodeUwDgfA20BalbcannMImmortalPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep1	Bladder - 1	bigWig 1.000000 626959.000000	Bladder A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	10	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Bladder A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Bladder - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=BLADDER rep=rep1\
track wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep1\
type bigWig 1.000000 626959.000000\

wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdSig	BMDM 8w Pol2	bigWig 0.110000 37.799999	BMDM Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	10	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel BMDM Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel BMDM 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrTfbsBmdmPol2FAdult8wksC57bl6StdSig\
type bigWig 0.110000 37.799999\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep2	BMDM 8wk Al 2	bam	BMDM Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	10	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel BMDM Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel BMDM 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=BMDM localization=CELL rnaExtract=PAP sex=F strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeLicrHistoneBmarrowH3k27acMAdult8wksC57bl6StdPk	BoneMarrow H3K27a	broadPeak	Bone Marrow 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	10	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Bone Marrow 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BoneMarrow H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBmarrowH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCaltechTfbsC2c12E2f4FCntrl50bE2p60hPcr1xSigRep1	C2 E2F4 60h 1	bigWig 0.059400 8322.877930	C2C12 E2F4 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	10	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 E2F4 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 E2F4 60h 1\
subGroups view=Signal factor=E2F4 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12E2f4FCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.059400 8322.877930\

wgEncodeCaltechHistC2c12H3ac06599FCntrl32bE2p24hPcr2xSigRep1	C2 H3ac 24h 1	bigWig 0.039500 1048.228760	C2C12 H3ac Myocyte 24h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	10	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3ac Myocyte 24h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 H3ac 24h 1\
subGroups view=Signal factor=H3AC06599 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechHistC2c12H3ac06599FCntrl32bE2p24hPcr2xSigRep1\
type bigWig 0.039500 1048.228760\

wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200AlnRep1	C2C12 Myob Aln	bam	C2C12 Myoblast RNA-seq Alignments from ENCODE/Caltech	0	10	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Myoblast RNA-seq Alignments from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewAlignments off\
shortLabel C2C12 Myob Aln\
subGroups view=Alignments cellType=cellC2C12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=NONE rep=rep1\
track wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200AlnRep1\
type bam\

wgEncodeSydhTfbsCh12CtcfbIggrabSig	CH12 CTCF	bigWig 1.000000 70041.000000	CH12 CTCF TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	10	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 CTCF TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig\
shortLabel CH12 CTCF\
subGroups view=Signal factor=CTCFb cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12CtcfbIggrabSig\
type bigWig 1.000000 70041.000000\

wgEncodePsuHistoneCh12H3k36me3FImmortal2a4bInputSig	CH12 H3K36m3	bigWig 1.000000 480.000000	CH12 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	10	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel CH12 H3K36m3\
subGroups view=Signal age=IMMORTAL factor=H3K36ME3 cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12H3k36me3FImmortal2a4bInputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:500\

wgEncodePsuTfbsErythroblInputBE14halfCd1InputSig	Erythrobl Input	bigWig 1.000000 118.000000	Erythroblast Input TFBS ChIP-seq Signal from ENCODE/PSU	2	10	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast Input TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel Erythrobl Input\
subGroups view=Signal age=E14HALF factor=zINPUT cellType=ERYTHROBL control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsErythroblInputBE14halfCd1InputSig\
type bigWig 1.000000 118.000000\

wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dAlnRep2	Erythroblast A 2	bam	Erythroblast 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU	0	10	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Erythroblast 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel Erythroblast A 2\
subGroups view=Alignments age=E14HALF cellType=ERYTHROBL readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqErythroblBE14halfCd1R2x99dAlnRep2\
type bam\

wgEncodeFsuRepliChipEsd3MDiffe3dWaveSignalRep2	ES-D3 EBM3 Ws 2	bigWig -13.418283 2.518819	ES-D3 EBM 3 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	10	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 EBM 3 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 EBM3 Ws 2\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=DIFFE3D rep=rep2\
track wgEncodeFsuRepliChipEsd3MDiffe3dWaveSignalRep2\
type bigWig -13.418283 2.518819\

wgEncodeSydhHistEse14InputStdSig	ES-E14 Input	bigWig 1.000000 255463.000000	ES-E14 Input Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	10	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 Input Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel ES-E14 Input\
subGroups view=Signal factor=zInputSTD cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhHistEse14InputStdSig\
type bigWig 1.000000 255463.000000\

phastCons30wayEuarch	Euarch Cons	wig 0 1	Euarchontoglires Conservation by PhastCons	0	10	10	70	10	70	10	10	0	0	0				compGeno	0	altColor 70,10,10\
autoScale off\
color 10,70,10\
configurable on\
longLabel Euarchontoglires Conservation by PhastCons\
maxHeightPixels 100:40:11\
noInherit on\
parent cons30wayViewphastcons off\
priority 10\
shortLabel Euarch Cons\
spanList 1\
subGroups view=phastcons clade=glires\
track phastCons30wayEuarch\
type wig 0 1\
windowingFunction mean\

polyASeqSitesTestisRev	PolyA-Seq Testis	bigWig 0.420000 12337.280273	Poly(A)-tail sequencing of Testis from Merck (Rev strand)	2	10	0	0	0	127	127	127	0	0	0				rna	0	color 0,0,0\
longLabel Poly(A)-tail sequencing of Testis from Merck (Rev strand)\
parent polyASeqSitesSignalView\
shortLabel PolyA-Seq Testis\
subGroups view=Signal tissType=Testis strand=rev\
track polyASeqSitesTestisRev\
type bigWig 0.420000 12337.280273\

wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep1	416B MR 1	bigWig 1.000000 61560.000000	416B Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	11	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel 416B MR 1\
subGroups view=MinusRawSignal age=IMMORTAL cellType=ACel416B localization=CELL rnaExtract=POLYA sex=M strain=B6D2F1J rep=rep1\
track wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep1\
type bigWig 1.000000 61560.000000\

wgEncodeUwDnase416bC57bl6MAdult8wksPkRep2	416B P 2	narrowPeak	416B DNaseI HS Peaks Rep 2 from ENCODE/UW	3	11	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel 416B DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel 416B P 2\
subGroups view=Peaks age=IMMORTAL cellType=A1416B sex=M strain=B6D2F1J rep=rep2 treatment=zNONE\
track wgEncodeUwDnase416bC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeUwDgfA20BalbcannMImmortalRawRep1	A20 Immt R	bigWig 1.000000 801343.000000	A20 Immortal BALB/cAnN DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	11	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 Immortal BALB/cAnN DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel A20 Immt R\
subGroups view=RawSignal age=IMMORTAL cellType=CelA20 strain=BALBCANN treatment=NONE rep=rep1\
track wgEncodeUwDgfA20BalbcannMImmortalRawRep1\
type bigWig 1.000000 801343.000000\

wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep1	Bladder + 1	bigWig 1.000000 908532.000000	Bladder A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	11	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Bladder A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Bladder + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=BLADDER rep=rep1\
track wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep1\
type bigWig 1.000000 908532.000000\

wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep1	BMDM 8wk Sg 1	bigWig 0.000000 64770.000000	BMDM Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	11	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel BMDM Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel BMDM 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=BMDM localization=CELL rnaExtract=PAP sex=F strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep1\
type bigWig 0.000000 64770.000000\

wgEncodeLicrHistoneBmarrowH3k27acMAdult8wksC57bl6StdSig	BoneMarrow H3K27a	bigWig 0.110000 49.990002	Bone Marrow 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	11	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Bone Marrow 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BoneMarrow H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBmarrowH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.110000 49.990002\
viewLimits 0.2:5\

wgEncodeCaltechTfbsC2c12Fosl1sc605FCntrl36bPcr1xPkRep1	C2 FOSL1 1	narrowPeak	C2C12 FOSL1 Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	11	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 FOSL1 Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 FOSL1 1\
subGroups view=Peaks factor=FOSL1SC605 cellType=C2C12 control=CNTRL36B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12Fosl1sc605FCntrl36bPcr1xPkRep1\
type narrowPeak\

wgEncodeCaltechHistC2c12H3ac06599FCntrl32bPcr2xPkRep1	C2 H3ac 1	narrowPeak	C2C12 H3ac Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	11	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3ac Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks off\
shortLabel C2 H3ac 1\
subGroups view=Peaks factor=H3AC06599 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12H3ac06599FCntrl32bPcr2xPkRep1\
type narrowPeak\

wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200RawRep1	C2C12 Myob Raw	bigWig 0.050000 836773.000000	C2C12 Myoblast RNA-seq Raw Signal from ENCODE/Caltech	2	11	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Myoblast RNA-seq Raw Signal from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewRawSignal\
shortLabel C2C12 Myob Raw\
subGroups view=RawSignal cellType=cellC2C12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=NONE rep=rep1\
track wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200RawRep1\
type bigWig 0.050000 836773.000000\

wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdPk	Cb 8w CTCF	broadPeak	Cerebellum Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	11	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks\
shortLabel Cb 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsCh12E2f4IggrabPk	CH12 E2F4	narrowPeak	CH12 E2F4 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	11	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 E2F4 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 E2F4\
subGroups view=Peaks factor=E2F4 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12E2f4IggrabPk\
type narrowPeak\

wgEncodePsuHistoneCh12InputFImmortal2a4bInputSig	CH12 Input	bigWig 1.000000 200.000000	CH12 Input Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	11	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Input Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel CH12 Input\
subGroups view=Signal age=IMMORTAL factor=zINPUT cellType=CH12 control=INPUT treatment=aNONE sex=F strain=s2A4B\
track wgEncodePsuHistoneCh12InputFImmortal2a4bInputSig\
type bigWig 1.000000 200.000000\

wgEncodeFsuRepliChipEsd3MDiffe6dWaveSignalRep1	ES-D3 EBM6 Ws 1	bigWig -10.554374 1.634434	ES-D3 EBM 6 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	11	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 EBM 6 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 EBM6 Ws 1\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=DIFFE6D rep=rep1\
track wgEncodeFsuRepliChipEsd3MDiffe6dWaveSignalRep1\
type bigWig -10.554374 1.634434\

wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dPlusRawRep1	FVL-stem P 1	bigWig 1.000000 685909.000000	FVL-stem 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	11	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel FVL-stem 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel FVL-stem P 1\
subGroups view=PlusRawSignal age=ADULT810WKS cellType=FVLS readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dPlusRawRep1\
type bigWig 1.000000 685909.000000\

wgEncodePsuTfbsG1eCtcfME0S129InputPk	G1E CTCF	broadPeak	G1E CTCF TFBS ChIP-seq Peaks from ENCODE/PSU	3	11	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E CTCF TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E CTCF\
subGroups view=Peaks age=E0 factor=CTCF cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eCtcfME0S129InputPk\
type broadPeak\

phastCons30wayPlacental	Mammal Cons	wig 0 1	Placental Mammal Conservation by PhastCons	0	11	10	70	10	70	10	10	0	0	0				compGeno	0	altColor 70,10,10\
autoScale off\
color 10,70,10\
configurable on\
longLabel Placental Mammal Conservation by PhastCons\
maxHeightPixels 100:40:11\
noInherit on\
parent cons30wayViewphastcons off\
priority 11\
shortLabel Mammal Cons\
spanList 1\
subGroups view=phastcons clade=mammal\
track phastCons30wayPlacental\
type wig 0 1\
windowingFunction mean\

wgEncodeSydhHistMelH3k04me1Dm2p5dStdPk	MEL H3K4m1 DMSO	narrowPeak	MEL H3K4me1 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	11	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K4me1 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks\
shortLabel MEL H3K4m1 DMSO\
subGroups view=Peaks factor=H3K04ME1 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k04me1Dm2p5dStdPk\
type narrowPeak\

wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep2	416B MR 2	bigWig 1.000000 44456.000000	416B Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	12	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel 416B MR 2\
subGroups view=MinusRawSignal age=IMMORTAL cellType=ACel416B localization=CELL rnaExtract=POLYA sex=M strain=B6D2F1J rep=rep2\
track wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jMinusRawRep2\
type bigWig 1.000000 44456.000000\

wgEncodeUwDnase416bC57bl6MAdult8wksSigRep2	416B S 2	bigWig 1.000000 74554.000000	416B DNaseI HS Signal Rep 2 from ENCODE/UW	2	12	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel 416B S 2\
subGroups view=Signal age=IMMORTAL cellType=A1416B sex=M strain=B6D2F1J rep=rep2 treatment=zNONE\
track wgEncodeUwDnase416bC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 74554.000000\

wgEncodeUwDgfA20BalbcannMImmortalSigRep1	A20 Immt S	bigWig 1.000000 143918.000000	A20 Immortal BALB/cAnN DNaseI DGF Signal Rep 1 from ENCODE/UW	2	12	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 Immortal BALB/cAnN DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel A20 Immt S\
subGroups view=Signal age=IMMORTAL cellType=CelA20 strain=BALBCANN treatment=NONE rep=rep1\
track wgEncodeUwDgfA20BalbcannMImmortalSigRep1\
type bigWig 1.000000 143918.000000\

wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep2	Bladder Aln 2	bam	Bladder A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	12	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Bladder A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Bladder Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=BLADDER rep=rep2\
track wgEncodeCshlLongRnaSeqBladderAdult8wksAlnRep2\
type bam\

wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep2	BMDM 8wk Sg 2	bigWig 0.000000 33962.000000	BMDM Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	12	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel BMDM Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel BMDM 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=BMDM localization=CELL rnaExtract=PAP sex=F strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqBmdmCellPapFAdult8wksC57bl6SigRep2\
type bigWig 0.000000 33962.000000\

wgEncodeLicrHistoneBmarrowInputMAdult8wksC57bl6StdSig	BoneMarrow Input	bigWig 0.150000 34.869999	Bone Marrow 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	12	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Bone Marrow 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BoneMarrow Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=B1MARROW control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBmarrowInputMAdult8wksC57bl6StdSig\
type bigWig 0.150000 34.869999\
viewLimits 0.2:5\

wgEncodeCaltechTfbsC2c12Fosl1sc605FCntrl36bPcr1xSigRep1	C2 FOSL1 1	bigWig 0.048800 5862.488770	C2C12 FOSL1 Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	12	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 FOSL1 Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 FOSL1 1\
subGroups view=Signal factor=FOSL1SC605 cellType=C2C12 control=CNTRL36B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12Fosl1sc605FCntrl36bPcr1xSigRep1\
type bigWig 0.048800 5862.488770\

wgEncodeCaltechHistC2c12H3ac06599FCntrl32bPcr2xSigRep1	C2 H3ac 1	bigWig 0.053000 696.133972	C2C12 H3ac Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	12	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3ac Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 H3ac 1\
subGroups view=Signal factor=H3AC06599 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12H3ac06599FCntrl32bPcr2xSigRep1\
type bigWig 0.053000 696.133972\

wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200SigRep1	C2C12 Myob Sig	bigWig 1.000000 756984.000000	C2C12 Myoblast RNA-seq Signal (Unique Reads) from ENCODE/Caltech	0	12	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Myoblast RNA-seq Signal (Unique Reads) from ENCODE/Caltech\
parent wgEncodeCaltechRnaSeqViewSignal off\
shortLabel C2C12 Myob Sig\
subGroups view=Signal cellType=cellC2C12 insertLength=IL200 mapAlgorithm=TH131 readType=R2X75 sex=F strain=C3H treatment=NONE rep=rep1\
track wgEncodeCaltechRnaSeqC2c12C3hFR2x75Th131Il200SigRep1\
type bigWig 1.000000 756984.000000\

wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdSig	Cb 8w CTCF	bigWig 0.110000 29.299999	Cerebellum Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	12	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal\
shortLabel Cb 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCbellumCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.110000 29.299999\
viewLimits 0.2:5\

wgEncodeSydhTfbsCh12E2f4IggrabSig	CH12 E2F4	bigWig 1 79444	CH12 E2F4 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	12	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 E2F4 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 E2F4\
subGroups view=Signal factor=E2F4 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12E2f4IggrabSig\
type bigWig 1 79444\

wgEncodePsuHistoneErythroblH3k04me1BE14halfCd1InputPk	Erythrob H3K4m1	broadPeak	Erythroblast H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	12	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Erythroblast H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Erythrob H3K4m1\
subGroups view=Peaks age=E14HALF factor=H3K04ME1 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k04me1BE14halfCd1InputPk\
type broadPeak\

wgEncodeFsuRepliChipEsd3MDiffe6dWaveSignalRep2	ES-D3 EBM6 Ws 2	bigWig -9.815218 2.047791	ES-D3 EBM 6 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	12	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 EBM 6 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 EBM6 Ws 2\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=DIFFE6D rep=rep2\
track wgEncodeFsuRepliChipEsd3MDiffe6dWaveSignalRep2\
type bigWig -9.815218 2.047791\

wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dMinusRawRep1	FVL-stem M 1	bigWig -683959.000000 -1.000000	FVL-stem 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	12	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel FVL-stem 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel FVL-stem M 1\
subGroups view=MinusRawSignal age=ADULT810WKS cellType=FVLS readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dMinusRawRep1\
type bigWig -683959.000000 -1.000000\

wgEncodePsuTfbsG1eCtcfME0S129InputSig	G1E CTCF	bigWig 1.000000 188.000000	G1E CTCF TFBS ChIP-seq Signal from ENCODE/PSU	2	12	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E CTCF TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E CTCF\
subGroups view=Signal age=E0 factor=CTCF cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eCtcfME0S129InputSig\
type bigWig 1.000000 188.000000\
viewLimits 1:50\

wgEncodeSydhHistMelH3k04me1IggrabPk	MEL H3K4m1 rab	narrowPeak	MEL H3K4me1 IgG-rab Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	12	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K4me1 IgG-rab Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks\
shortLabel MEL H3K4m1 rab\
subGroups view=Peaks factor=H3K04ME1 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhHistMelH3k04me1IggrabPk\
type narrowPeak\

phastCons30way	Vertebrate Cons	wig 0 1	Vertebrate Conservation by PhastCons	0	12	10	70	10	70	10	10	0	0	0				compGeno	0	altColor 70,10,10\
autoScale off\
color 10,70,10\
configurable on\
longLabel Vertebrate Conservation by PhastCons\
maxHeightPixels 100:40:11\
noInherit on\
parent cons30wayViewphastcons off\
priority 12\
shortLabel Vertebrate Cons\
spanList 1\
subGroups view=phastcons clade=vert\
track phastCons30way\
type wig 0 1\
windowingFunction mean\

wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep1	416B PR 1	bigWig 1.000000 74282.000000	416B Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	13	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel 416B PR 1\
subGroups view=PlusRawSignal age=IMMORTAL cellType=ACel416B localization=CELL rnaExtract=POLYA sex=M strain=B6D2F1J rep=rep1\
track wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep1\
type bigWig 1.000000 74282.000000\

wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep1	A20 H 1	broadPeak	A20 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	13	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel A20 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel A20 H 1\
subGroups view=Hotspots age=IMMORTAL cellType=A20 sex=M strain=BALBCANN rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksHotspotsRep1	Bcell CD19+ 8w H	broadPeak	B-cell (CD19+) 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	13	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD19+) 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel Bcell CD19+ 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=CelBCELLCD19P strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep2	Bladder - 2	bigWig 1.000000 398901.000000	Bladder A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	13	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Bladder A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Bladder - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=BLADDER rep=rep2\
track wgEncodeCshlLongRnaSeqBladderAdult8wksMinusRawRep2\
type bigWig 1.000000 398901.000000\

wgEncodeLicrHistoneBmdmH3k04me1FAdult8wksC57bl6StdPk	BMDM H3K4m1	broadPeak	BMDM 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	13	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel BMDM 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BMDM H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneBmdmH3k04me1FAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCaltechTfbsC2c12InputFCntrl32bE2p24hPcr2xSigRep1	C2 Con 32bp 24h 1	bigWig 0.086100 1009.830200	C2C12 Control 32bp Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	13	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Control 32bp Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Con 32bp 24h 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechTfbsC2c12InputFCntrl32bE2p24hPcr2xSigRep1\
type bigWig 0.086100 1009.830200\

wgEncodeCaltechHistC2c12H3k04me3FCntrl50bE2p60hPcr1xPkRep1	C2 H3K4me3 60h 1	narrowPeak	C2C12 H3K4me3 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	13	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K4me3 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks\
shortLabel C2 H3K4me3 60h 1\
subGroups view=Peaks factor=H3K04ME3 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12H3k04me3FCntrl50bE2p60hPcr1xPkRep1\
type narrowPeak\

wgEncodeLicrTfbsCbellumInputMAdult8wksC57bl6StdSig	Cb 8w Input	bigWig 0.140000 41.009998	Cerebellum Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	13	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Cb 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCbellumInputMAdult8wksC57bl6StdSig\
type bigWig 0.140000 41.009998\

wgEncodeSydhTfbsCh12Ets1IggrabPk	CH12 ETS1	narrowPeak	CH12 ETS1 ChIP-seq Peaks from ENCODE/Stanford/Yale	3	13	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 ETS1 ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 ETS1\
subGroups view=Peaks factor=ETS1 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Ets1IggrabPk\
type narrowPeak\

wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep1	Crbellum 8wk Al 1	bam	Cerebellum Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	13	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Crbellum 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodePsuHistoneErythroblH3k04me1BE14halfCd1InputSig	Erythrob H3K4m1	bigWig 1.000000 480.000000	Erythroblast H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	13	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Erythrob H3K4m1\
subGroups view=Signal age=E14HALF factor=H3K04ME1 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k04me1BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:400\

wgEncodeFsuRepliChipEsd3MDiffe9dWaveSignalRep1	ES-D3 NP Ws 1	bigWig -7.040370 1.677722	ES-D3 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	13	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 NP Ws 1\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=DIFFE9D rep=rep1\
track wgEncodeFsuRepliChipEsd3MDiffe9dWaveSignalRep1\
type bigWig -7.040370 1.677722\

wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dAlnRep1	FVL-stem A 1	bam	FVL-stem 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU	0	13	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel FVL-stem 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel FVL-stem A 1\
subGroups view=Alignments age=ADULT810WKS cellType=FVLS readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dAlnRep1\
type bam\

wgEncodePsuTfbsG1eGata1aME0S129InputPk	G1E GATA1	broadPeak	G1E GATA1 TFBS ChIP-seq Peaks from ENCODE/PSU	3	13	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E GATA1 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E GATA1\
subGroups view=Peaks age=E0 factor=GATA1a cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eGata1aME0S129InputPk\
type broadPeak\

wgEncodeSydhHistMelH3k04me1Dm2p5dStdSig	MEL H3K4m1 DMSO	bigWig 1.000000 31847.000000	MEL H3K4me1 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	13	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K4me1 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig\
shortLabel MEL H3K4m1 DMSO\
subGroups view=Signal factor=H3K04ME1 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k04me1Dm2p5dStdSig\
type bigWig 1.000000 31847.000000\

wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep2	416B PR 2	bigWig 1.000000 139390.000000	416B Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	14	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel 416B PR 2\
subGroups view=PlusRawSignal age=IMMORTAL cellType=ACel416B localization=CELL rnaExtract=POLYA sex=M strain=B6D2F1J rep=rep2\
track wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jPlusRawRep2\
type bigWig 1.000000 139390.000000\

wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep1	A20 P 1	narrowPeak	A20 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	14	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel A20 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel A20 P 1\
subGroups view=Peaks age=IMMORTAL cellType=A20 sex=M strain=BALBCANN rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep1\
type narrowPeak\

wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksPkRep1	Bcell CD19+ 8w P	narrowPeak	B-cell (CD19+) 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	14	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD19+) 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel Bcell CD19+ 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=CelBCELLCD19P strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep2	Bladder + 2	bigWig 1.000000 784114.000000	Bladder A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	14	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Bladder A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Bladder + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=BLADDER rep=rep2\
track wgEncodeCshlLongRnaSeqBladderAdult8wksPlusRawRep2\
type bigWig 1.000000 784114.000000\

wgEncodeLicrHistoneBmdmH3k04me1FAdult8wksC57bl6StdSig	BMDM H3K4m1	bigWig 0.110000 9.030000	BMDM 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	14	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel BMDM 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BMDM H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneBmdmH3k04me1FAdult8wksC57bl6StdSig\
type bigWig 0.110000 9.030000\
viewLimits 0.2:3\

wgEncodeCaltechTfbsC2c12InputFCntrl32bE2p60hPcr2xSigRep1	C2 Con 32bp 60h 1	bigWig 0.042600 2602.975830	C2C12 Control 32bp Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	14	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Control 32bp Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Con 32bp 60h 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12InputFCntrl32bE2p60hPcr2xSigRep1\
type bigWig 0.042600 2602.975830\

wgEncodeCaltechHistC2c12H3k04me3FCntrl50bE2p60hPcr1xSigRep1	C2 H3K4me3 60h 1	bigWig 0.034800 6329.222168	C2C12 H3K4me3 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	14	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3K4me3 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal\
shortLabel C2 H3K4me3 60h 1\
subGroups view=Signal factor=H3K04ME3 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12H3k04me3FCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.034800 6329.222168\

wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdPk	Cb 8w Pol2	broadPeak	Cerebellum Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	14	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks\
shortLabel Cb 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsCh12Ets1IggrabSig	CH12 ETS1	bigWig 1.000000 99081.000000	CH12 ETS1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	14	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 ETS1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 ETS1\
subGroups view=Signal factor=ETS1 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Ets1IggrabSig\
type bigWig 1.000000 99081.000000\

wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep2	Crbellum 8wk Al 2	bam	Cerebellum Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	14	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Crbellum 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodePsuHistoneErythroblH3k04me3BE14halfCd1InputPk	Erythrob H3K4m3	broadPeak	Erythroblast H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	14	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Erythroblast H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Erythrob H3K4m3\
subGroups view=Peaks age=E14HALF factor=H3K04ME3 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k04me3BE14halfCd1InputPk\
type broadPeak\

wgEncodeFsuRepliChipEsd3MDiffe9dWaveSignalRep2	ES-D3 NP Ws 2	bigWig -8.892423 1.362410	ES-D3 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	14	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 NP Ws 2\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=DIFFE9D rep=rep2\
track wgEncodeFsuRepliChipEsd3MDiffe9dWaveSignalRep2\
type bigWig -8.892423 1.362410\

wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dPlusRawRep2	FVL-stem P 2	bigWig 1.000000 2349197.000000	FVL-stem 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	14	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel FVL-stem 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel FVL-stem P 2\
subGroups view=PlusRawSignal age=ADULT810WKS cellType=FVLS readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dPlusRawRep2\
type bigWig 1.000000 2349197.000000\

wgEncodePsuTfbsG1eGata1aME0S129InputSig	G1E GATA1	bigWig 1.000000 104.000000	G1E GATA1 TFBS ChIP-seq Signal from ENCODE/PSU	2	14	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E GATA1 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E GATA1\
subGroups view=Signal age=E0 factor=GATA1a cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eGata1aME0S129InputSig\
type bigWig 1.000000 104.000000\
viewLimits 2:150\

wgEncodeSydhHistMelH3k04me1IggrabSig	MEL H3K4m1 rab	bigWig 1.000000 36358.000000	MEL H3K4me1 IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	14	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K4me1 IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig\
shortLabel MEL H3K4m1 rab\
subGroups view=Signal factor=H3K04ME1 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhHistMelH3k04me1IggrabSig\
type bigWig 1.000000 36358.000000\

wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep1	416B S 1	bigWig 1.000000 74282.000000	416B Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW	2	15	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel 416B S 1\
subGroups view=Signal age=IMMORTAL cellType=ACel416B localization=CELL rnaExtract=POLYA sex=M strain=B6D2F1J rep=rep1\
track wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep1\
type bigWig 1.000000 74282.000000\

wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep1	A20 S 1	bigWig 1.000000 93407.000000	A20 DNaseI HS Signal Rep 1 from ENCODE/UW	2	15	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel A20 S 1\
subGroups view=Signal age=IMMORTAL cellType=A20 sex=M strain=BALBCANN rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep1\
type bigWig 1.000000 93407.000000\

wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksRawRep1	Bcell CD19+ 8w R	bigWig 1.000000 785440.000000	B-cell (CD19+) 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	15	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD19+) 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel Bcell CD19+ 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=CelBCELLCD19P strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 785440.000000\

wgEncodeCshlLongRnaSeqBladderAdult8wksContigs	Bladder C	bed 6 +	Bladder A8 Long RNA-seq Contigs from ENCODE/CSHL	3	15	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Bladder A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Bladder C\
subGroups view=Contigs age=ADULT8WKS cellType=BLADDER rep=repP\
track wgEncodeCshlLongRnaSeqBladderAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneBmdmH3k04me3FAdult8wksC57bl6StdPk	BMDM H3K4m3	broadPeak	BMDM 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	15	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel BMDM 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BMDM H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneBmdmH3k04me3FAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCaltechTfbsC2c12InputFCntrl32bPcr2xSigRep1	C2 Con 32bp  1	bigWig 0.077700 1187.887817	C2C12 Control 32bp Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	15	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Control 32bp Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Con 32bp  1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12InputFCntrl32bPcr2xSigRep1\
type bigWig 0.077700 1187.887817\

wgEncodeCaltechHistC2c12H3k04me3FCntrl50bPcr1xPkRep1	C2 H3K4me3 1	narrowPeak	C2C12 H3K4me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	15	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K4me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks\
shortLabel C2 H3K4me3 1\
subGroups view=Peaks factor=H3K04ME3 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12H3k04me3FCntrl50bPcr1xPkRep1\
type narrowPeak\

wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdSig	Cb 8w Pol2	bigWig 0.150000 52.380001	Cerebellum Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	15	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal\
shortLabel Cb 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCbellumPol2MAdult8wksC57bl6StdSig\
type bigWig 0.150000 52.380001\
viewLimits 0.2:3\

wgEncodeSydhTfbsCh12Gcn5IggrabPk	CH12 GCN5 P	narrowPeak	CH12 GCN5 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	15	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 GCN5 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 GCN5 P\
subGroups view=Peaks factor=GCN5 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Gcn5IggrabPk\
type narrowPeak\

wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep1	Crbellum 8wk Sg 1	bigWig 3.000000 65524.000000	Cerebellum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	15	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel Crbellum 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep1\
type bigWig 3.000000 65524.000000\

wgEncodePsuHistoneErythroblH3k04me3BE14halfCd1InputSig	Erythrob H3K4m3	bigWig 1.000000 480.000000	Erythroblast H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	15	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Erythrob H3K4m3\
subGroups view=Signal age=E14HALF factor=H3K04ME3 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k04me3BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:500\

wgEncodeFsuRepliChipEsd3MDiffg3dWaveSignalRep1	ES-D3 EPL Ws 1	bigWig -4.491621 2.001237	ES-D3 EPL 3 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	15	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 EPL 3 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 EPL Ws 1\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=DIFFG3D rep=rep1\
track wgEncodeFsuRepliChipEsd3MDiffg3dWaveSignalRep1\
type bigWig -4.491621 2.001237\

wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dMinusRawRep2	FVL-stem M 2	bigWig -2309090.000000 -1.000000	FVL-stem 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	15	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel FVL-stem 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel FVL-stem M 2\
subGroups view=MinusRawSignal age=ADULT810WKS cellType=FVLS readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dMinusRawRep2\
type bigWig -2309090.000000 -1.000000\

wgEncodePsuTfbsG1eGata2sc9008ME0S129InputPk	G1E GATA2	broadPeak	G1E GATA2 TFBS ChIP-seq Peaks from ENCODE/PSU	3	15	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E GATA2 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E GATA2\
subGroups view=Peaks age=E0 factor=GATA2SC9008 cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eGata2sc9008ME0S129InputPk\
type broadPeak\

wgEncodeSydhHistMelH3k04me3Dm2p5dStdPk	MEL H3K4m3 DMSO	narrowPeak	MEL H3K4me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	15	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K4me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks\
shortLabel MEL H3K4m3 DMSO\
subGroups view=Peaks factor=H3K04ME3 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k04me3Dm2p5dStdPk\
type narrowPeak\

wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep2	416B S 2	bigWig 1.000000 139390.000000	416B Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW	2	16	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel 416B Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel 416B S 2\
subGroups view=Signal age=IMMORTAL cellType=ACel416B localization=CELL rnaExtract=POLYA sex=M strain=B6D2F1J rep=rep2\
track wgEncodeUwRnaSeq416bCellPolyaMImmortalB6d2f1jSigRep2\
type bigWig 1.000000 139390.000000\

wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep2	A20 H 2	broadPeak	A20 DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	16	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel A20 DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel A20 H 2\
subGroups view=Hotspots age=IMMORTAL cellType=A20 sex=M strain=BALBCANN rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseA20BalbcannMAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksSigRep1	Bcell CD19+ 8w S	bigWig 1.000000 102599.000000	B-cell (CD19+) 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	16	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD19+) 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel Bcell CD19+ 8w S\
subGroups view=Signal age=ADULT8WKS cellType=CelBCELLCD19P strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfBcellcd19pC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 102599.000000\

wgEncodeCshlLongRnaSeqBladderAdult8wksJunctions	Bladder J	bed 6 +	Bladder A8 Long RNA-seq Junctions from ENCODE/CSHL	0	16	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Bladder A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Bladder J\
subGroups view=SJunctions age=ADULT8WKS cellType=BLADDER rep=repP\
track wgEncodeCshlLongRnaSeqBladderAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneBmdmH3k04me3FAdult8wksC57bl6StdSig	BMDM H3K4m3	bigWig 0.110000 77.830002	BMDM 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	16	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel BMDM 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BMDM H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneBmdmH3k04me3FAdult8wksC57bl6StdSig\
type bigWig 0.110000 77.830002\
viewLimits 0.2:10\

wgEncodeCaltechTfbsC2c12InputFCntrl36bPcr1xSigRep1	C2 Con 36bp 1	bigWig 0.042412 6022.777344	C2C12 Control 36bp ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	16	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Control 36bp ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Con 36bp 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL36B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12InputFCntrl36bPcr1xSigRep1\
type bigWig 0.042412 6022.777344\

wgEncodeCaltechHistC2c12H3k04me3FCntrl50bPcr1xSigRep1	C2 H3K4me3 1	bigWig 0.040800 7083.820801	C2C12 H3K4me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	16	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3K4me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal\
shortLabel C2 H3K4me3 1\
subGroups view=Signal factor=H3K04ME3 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12H3k04me3FCntrl50bPcr1xSigRep1\
type bigWig 0.040800 7083.820801\

wgEncodeSydhTfbsCh12Gcn5IggrabSig	CH12 GCN5 S	bigWig 1.000000 160336.000000	CH12 GCN5 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	16	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 GCN5 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 GCN5 S\
subGroups view=Signal factor=GCN5 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Gcn5IggrabSig\
type bigWig 1.000000 160336.000000\

wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdPk	Cortex 8w CTCF	broadPeak	Cortex Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	16	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Cortex 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep2	Crbellum 8wk Sg 2	bigWig 3.000000 65534.000000	Cerebellum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	16	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel Crbellum 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqCbellumCellPapMAdult8wksC57bl6SigRep2\
type bigWig 3.000000 65534.000000\

wgEncodePsuHistoneErythroblH3k09me3BE14halfCd1InputPk	Erythrob H3K9m3	broadPeak	Erythroblast H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	16	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Erythroblast H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Erythrob H3K9m3\
subGroups view=Peaks age=E14HALF factor=H3K09ME3 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k09me3BE14halfCd1InputPk\
type broadPeak\

wgEncodeFsuRepliChipEsd3MDiffg3dWaveSignalRep2	ES-D3 EPL Ws 2	bigWig -7.767494 2.185306	ES-D3 EPL 3 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	16	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 EPL 3 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 EPL Ws 2\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=DIFFG3D rep=rep2\
track wgEncodeFsuRepliChipEsd3MDiffg3dWaveSignalRep2\
type bigWig -7.767494 2.185306\

wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dAlnRep2	FVL-stem A 2	bam	FVL-stem 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU	0	16	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel FVL-stem 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel FVL-stem A 2\
subGroups view=Alignments age=ADULT810WKS cellType=FVLS readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqFvlsBAdult810wksBalbcjR2x99dAlnRep2\
type bam\

wgEncodePsuTfbsG1eGata2sc9008ME0S129InputSig	G1E GATA2	bigWig 1.000000 128.000000	G1E GATA2 TFBS ChIP-seq Signal from ENCODE/PSU	2	16	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E GATA2 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E GATA2\
subGroups view=Signal age=E0 factor=GATA2SC9008 cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eGata2sc9008ME0S129InputSig\
type bigWig 1.000000 128.000000\
viewLimits 2:20\

wgEncodeSydhHistMelH3k04me3Dm2p5dIggyalePk	MEL H3K4m3 DMSO Y	narrowPeak	MEL H3K4me3 DMSO 2% IgG-Yale Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	16	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K4me3 DMSO 2% IgG-Yale Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks\
shortLabel MEL H3K4m3 DMSO Y\
subGroups view=Peaks factor=H3K04ME3 cellType=MEL control=IGGYale treatment=DM2P5D\
track wgEncodeSydhHistMelH3k04me3Dm2p5dIggyalePk\
type narrowPeak\

wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep2	A20 P 2	narrowPeak	A20 DNaseI HS Peaks Rep 2 from ENCODE/UW	3	17	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel A20 DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel A20 P 2\
subGroups view=Peaks age=IMMORTAL cellType=A20 sex=M strain=BALBCANN rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseA20BalbcannMAdult8wksPkRep2\
type narrowPeak\

wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6AlnRep1	B_(CD19+) 8w A 1	bam	B-cell (CD19+) Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	17	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD19+) Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel B_(CD19+) 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=BCELLCD19P localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksHotspotsRep1	Bcell CD43- 8w H	broadPeak	B-cell (CD43-) 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	17	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel Bcell CD43- 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=CelBCELLCD43N strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneBmdmH3k27acFAdult8wksC57bl6StdPk	BMDM H3K27a	broadPeak	BMDM 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	17	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel BMDM 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BMDM H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneBmdmH3k27acFAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCaltechTfbsC2c12InputFCntrl50bE2p60hPcr1xSigRep1	C2 Con 50bp 60h 1	bigWig 0.052000 10580.088867	C2C12 Control 50bp Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	17	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Control 50bp Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Con 50bp 60h 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12InputFCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.052000 10580.088867\

wgEncodeCaltechHistC2c12H3k27me3FCntrl32bE2p60hPcr2xPkRep1	C2 H3K27me3 60h 1	narrowPeak	C2C12 H3K27me3 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	17	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K27me3 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks off\
shortLabel C2 H3K27me3 60h 1\
subGroups view=Peaks factor=H3K27ME3 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12H3k27me3FCntrl32bE2p60hPcr2xPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep1	Cerebellum Aln 1	bam	Cerebellum A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	17	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Cerebellum Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=CBELLUM rep=rep1\
track wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep1\
type bam\

wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabPk	CH12 HCFC1 P	narrowPeak	CH12 HCFC1 (NB100-68209) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	17	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 HCFC1 (NB100-68209) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 HCFC1 P\
subGroups view=Peaks factor=HCFC1NB10068209 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabPk\
type narrowPeak\

wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdSig	Cortex 8w CTCF	bigWig 0.130000 58.930000	Cortex Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	17	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Cortex 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCortexCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.130000 58.930000\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep1	Cortex 8wk Al 1	bam	Cortex Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	17	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Cortex 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=CORTEX localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodePsuHistoneErythroblH3k09me3BE14halfCd1InputSig	Erythrob H3K9m3	bigWig 1.000000 480.000000	Erythroblast H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	17	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Erythrob H3K9m3\
subGroups view=Signal age=E14HALF factor=H3K09ME3 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k09me3BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:150\

wgEncodeFsuRepliChipEsd3MWaveSignalRep1	ES-D3 Ws 1	bigWig -6.216455 1.621844	ES-D3 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	17	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 Ws 1\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipEsd3MWaveSignalRep1\
type bigWig -6.216455 1.621844\

wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dPlusRawRep1	FV-progenitor P 1	bigWig 1.000000 1818803.000000	FV-progenitor 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	17	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel FV-progenitor 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel FV-progenitor P 1\
subGroups view=PlusRawSignal age=ADULT810WKS cellType=FVP readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dPlusRawRep1\
type bigWig 1.000000 1818803.000000\

wgEncodePsuTfbsG1ePol24h8ME0S129InputPk	G1E Pol2	broadPeak	G1E Pol2-4H8 TFBS ChIP-seq Peaks from ENCODE/PSU	3	17	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E Pol2-4H8 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E Pol2\
subGroups view=Peaks age=E0 factor=POL24H8 cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1ePol24h8ME0S129InputPk\
type broadPeak\

wgEncodeSydhHistMelH3k04me3IggrabPk	MEL H3K4m3 rab	narrowPeak	MEL H3K4me3 IgG-rab Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	17	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K4me3 IgG-rab Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks\
shortLabel MEL H3K4m3 rab\
subGroups view=Peaks factor=H3K04ME3 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhHistMelH3k04me3IggrabPk\
type narrowPeak\

wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep2	A20 S 2	bigWig 1.000000 162688.000000	A20 DNaseI HS Signal Rep 2 from ENCODE/UW	2	18	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel A20 DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel A20 S 2\
subGroups view=Signal age=IMMORTAL cellType=A20 sex=M strain=BALBCANN rep=rep2  treatment=zNONE\
track wgEncodeUwDnaseA20BalbcannMAdult8wksSigRep2\
type bigWig 1.000000 162688.000000\

wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6MinusRawRep1	B_(CD19+) 8w MR 1	bigWig 1.000000 168798.000000	B-cell (CD19+) Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	18	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD19+) Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel B_(CD19+) 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=BCELLCD19P localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 168798.000000\

wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksPkRep1	Bcell CD43- 8w P	narrowPeak	B-cell (CD43-) 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	18	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel Bcell CD43- 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=CelBCELLCD43N strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeLicrHistoneBmdmH3k27acFAdult8wksC57bl6StdSig	BMDM H3K27a	bigWig 0.110000 57.849998	BMDM 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	18	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel BMDM 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BMDM H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneBmdmH3k27acFAdult8wksC57bl6StdSig\
type bigWig 0.110000 57.849998\
viewLimits 0.2:5\

wgEncodeCaltechTfbsC2c12InputFCntrl50bE2p60hPcr1xSigRep2	C2 Con 50bp 60h 2	bigWig 0.032500 9851.844727	C2C12 Control 50bp Myocyte 60h TFBS ChIP-seq Signal Rep 2 from ENCODE/Caltech	2	18	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Control 50bp Myocyte 60h TFBS ChIP-seq Signal Rep 2 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Con 50bp 60h 2\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep2\
track wgEncodeCaltechTfbsC2c12InputFCntrl50bE2p60hPcr1xSigRep2\
type bigWig 0.032500 9851.844727\

wgEncodeCaltechHistC2c12H3k27me3FCntrl32bE2p60hPcr2xSigRep1	C2 H3K27me3 60h 1	bigWig 0.041100 776.236816	C2C12 H3K27me3 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	18	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3K27me3 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 H3K27me3 60h 1\
subGroups view=Signal factor=H3K27ME3 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12H3k27me3FCntrl32bE2p60hPcr2xSigRep1\
type bigWig 0.041100 776.236816\

wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep1	Cerebellum - 1	bigWig 1.000000 578586.000000	Cerebellum A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	18	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Cerebellum - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=CBELLUM rep=rep1\
track wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep1\
type bigWig 1.000000 578586.000000\

wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabSig	CH12 HCFC1 S	bigWig 1.000000 54808.000000	CH12 HCFC1 (NB100-68209) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	18	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 HCFC1 (NB100-68209) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 HCFC1 S\
subGroups view=Signal factor=HCFC1NB10068209 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Hcfc1nb10068209IggrabSig\
type bigWig 1.000000 54808.000000\

wgEncodeLicrTfbsCortexInputMAdult8wksC57bl6StdSig	Cortex 8w Input	bigWig 0.130000 61.080002	Cortex Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	18	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Cortex 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCortexInputMAdult8wksC57bl6StdSig\
type bigWig 0.130000 61.080002\

wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep2	Cortex 8wk Al 2	bam	Cortex Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	18	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Cortex 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=CORTEX localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodePsuHistoneErythroblH3k27me3BE14halfCd1InputPk	Erythrob H3K27m3	broadPeak	Erythroblast H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	18	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Erythroblast H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Erythrob H3K27m3\
subGroups view=Peaks age=E14HALF factor=H3K27ME3 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k27me3BE14halfCd1InputPk\
type broadPeak\

wgEncodeFsuRepliChipEsd3MWaveSignalRep2	ES-D3 Ws 2	bigWig -2.013756 1.882734	ES-D3 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	18	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-D3 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-D3 Ws 2\
subGroups view=WaveSignal cellType=ESD3 sex=M treatment=NONE rep=rep2\
track wgEncodeFsuRepliChipEsd3MWaveSignalRep2\
type bigWig -2.013756 1.882734\

wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dMinusRawRep1	FV-progenitor M 1	bigWig -1556197.000000 -1.000000	FV-progenitor 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	18	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel FV-progenitor 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel FV-progenitor M 1\
subGroups view=MinusRawSignal age=ADULT810WKS cellType=FVP readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dMinusRawRep1\
type bigWig -1556197.000000 -1.000000\

wgEncodePsuTfbsG1ePol24h8ME0S129InputSig	G1E Pol2	bigWig 1.000000 346.000000	G1E Pol2-4H8 TFBS ChIP-seq Signal from ENCODE/PSU	2	18	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E Pol2-4H8 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E Pol2\
subGroups view=Signal age=E0 factor=POL24H8 cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1ePol24h8ME0S129InputSig\
type bigWig 1.000000 346.000000\
viewLimits 5:50\

wgEncodeSydhHistMelH3k04me3IggyalePk	MEL H3K4m3 Y	narrowPeak	MEL H3K4me3 IgG-Yale Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	18	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K4me3 IgG-Yale Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks\
shortLabel MEL H3K4m3 Y\
subGroups view=Peaks factor=H3K04ME3 cellType=MEL control=IGGYale treatment=zNONE\
track wgEncodeSydhHistMelH3k04me3IggyalePk\
type narrowPeak\

wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6PlusRawRep1	B_(CD19+) 8w PR 1	bigWig 1.000000 92881.000000	B-cell (CD19+) Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	19	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD19+) Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel B_(CD19+) 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=BCELLCD19P localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 92881.000000\

wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep1	Bcell (CD19+) H 1	broadPeak	B-cell (CD19+) DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	19	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD19+) DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots\
shortLabel Bcell (CD19+) H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=BCELLCD19P sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksRawRep1	Bcell CD43- 8w R	bigWig 1.000000 395435.000000	B-cell (CD43-) 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	19	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel Bcell CD43- 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=CelBCELLCD43N strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 395435.000000\

wgEncodeLicrHistoneBmdmInputFAdult8wksC57bl6StdSig	BMDM Input	bigWig 0.140000 48.919998	BMDM 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	19	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel BMDM 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BMDM Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=B1MDM control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneBmdmInputFAdult8wksC57bl6StdSig\
type bigWig 0.140000 48.919998\
viewLimits 0.2:5\

wgEncodeCaltechTfbsC2c12InputFCntrl50bPcr1xSigRep1	C2 Con 50bp 1	bigWig 0.073500 10874.264648	C2C12 Control 50bp Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	19	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Control 50bp Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Con 50bp 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12InputFCntrl50bPcr1xSigRep1\
type bigWig 0.073500 10874.264648\

wgEncodeCaltechHistC2c12H3k27me3FCntrl32bPcr2xPkRep1	C2 H3K27me3 1	narrowPeak	C2C12 H3K27me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	19	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K27me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks off\
shortLabel C2 H3K27me3 1\
subGroups view=Peaks factor=H3K27ME3 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12H3k27me3FCntrl32bPcr2xPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep1	Cerebellum + 1	bigWig 1.000000 864867.000000	Cerebellum A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	19	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Cerebellum + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=CBELLUM rep=rep1\
track wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep1\
type bigWig 1.000000 864867.000000\

wgEncodeSydhTfbsCh12JundIggrabPk	CH12 JunD P	narrowPeak	CH12 JunD TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	19	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 JunD TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 JunD P\
subGroups view=Peaks factor=JUND cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12JundIggrabPk\
type narrowPeak\

wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdPk	Cortex 8w Pol2	broadPeak	Cortex Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	19	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Cortex 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep1	Cortex 8wk Sg 1	bigWig 4.000000 65424.000000	Cortex Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	19	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Cortex 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=CORTEX localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep1\
type bigWig 4.000000 65424.000000\

wgEncodePsuHistoneErythroblH3k27me3BE14halfCd1InputSig	Erythrob H3K27m3	bigWig 1.000000 480.000000	Erythroblast H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	19	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Erythrob H3K27m3\
subGroups view=Signal age=E14HALF factor=H3K27ME3 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k27me3BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:500\

wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dAlnRep1	FV-progenitor A 1	bam	FV-progenitor 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU	0	19	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel FV-progenitor 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel FV-progenitor A 1\
subGroups view=Alignments age=ADULT810WKS cellType=FVP readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dAlnRep1\
type bam\

wgEncodePsuTfbsG1eTal1ME0S129InputPk	G1E TAL1	broadPeak	G1E TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU	3	19	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks\
shortLabel G1E TAL1\
subGroups view=Peaks age=E0 factor=TAL1 cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eTal1ME0S129InputPk\
type broadPeak\

wgEncodeSydhHistMelH3k04me3Dm2p5dStdSig	MEL H3K4m3 DMSO	bigWig 1.000000 27020.000000	MEL H3K4me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	19	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K4me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig\
shortLabel MEL H3K4m3 DMSO\
subGroups view=Signal factor=H3K04ME3 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k04me3Dm2p5dStdSig\
type bigWig 1.000000 27020.000000\

wgEncodeFsuRepliChipEsem5sUDiffhsoxmWaveSignalRep1	Mesoderm Ws 1	bigWig -6.037550 2.512868	Mesoderm Gsc/Sox17- Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	19	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel Mesoderm Gsc/Sox17- Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel Mesoderm Ws 1\
subGroups view=WaveSignal cellType=ESEM5S sex=U treatment=DIFFHSOXM rep=rep1\
track wgEncodeFsuRepliChipEsem5sUDiffhsoxmWaveSignalRep1\
type bigWig -6.037550 2.512868\

wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6SigRep1	B_(CD19+) 8w S 1	bigWig 1.000000 168799.000000	B-cell (CD19+) Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	20	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD19+) Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel B_(CD19+) 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=BCELLCD19P localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqBcellcd19pCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 168799.000000\

wgEncodeLicrHistoneBatH3k04me1MAdult24wksC57bl6StdPk	BAT 24w H3K4m1	broadPeak	Brown Adipose Tissue 24w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	20	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Brown Adipose Tissue 24w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BAT 24w H3K4m1\
subGroups view=Peaks age=A2DULT24WKS factor=H3K04ME1 cellType=BAT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBatH3k04me1MAdult24wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep1	Bcell (CD19+) P 1	narrowPeak	B-cell (CD19+) DNaseI HS Peaks Rep 1 from ENCODE/UW	3	20	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD19+) DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks\
shortLabel Bcell (CD19+) P 1\
subGroups view=Peaks age=ADULT8WKS cellType=BCELLCD19P sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksSigRep1	Bcell CD43- 8w S	bigWig 1.000000 62266.000000	B-cell (CD43-) 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	20	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel Bcell CD43- 8w S\
subGroups view=Signal age=ADULT8WKS cellType=CelBCELLCD43N strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfBcellcd43nC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 62266.000000\

wgEncodeCaltechHistC2c12H3k27me3FCntrl32bPcr2xSigRep1	C2 H3K27me3 1	bigWig 0.039600 738.758484	C2C12 H3K27me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	20	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3K27me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 H3K27me3 1\
subGroups view=Signal factor=H3K27ME3 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12H3k27me3FCntrl32bPcr2xSigRep1\
type bigWig 0.039600 738.758484\

wgEncodeCaltechTfbsC2c12MaxFCntrl50bE2p60hPcr1xPkRep1	C2 Max 60h 1	narrowPeak	C2C12 Max Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	20	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Max Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 Max 60h 1\
subGroups view=Peaks factor=MAX cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12MaxFCntrl50bE2p60hPcr1xPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep2	Cerebellum Aln 2	bam	Cerebellum A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	20	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Cerebellum Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=CBELLUM rep=rep2\
track wgEncodeCshlLongRnaSeqCbellumAdult8wksAlnRep2\
type bam\

wgEncodeSydhTfbsCh12JundIggrabSig	CH12 JunD	bigWig 1 63771	CH12 JunD TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	20	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 JunD TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 JunD\
subGroups view=Signal factor=JUND cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12JundIggrabSig\
type bigWig 1 63771\

wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdSig	Cortex 8w Pol2	bigWig 0.110000 40.849998	Cortex Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	20	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Cortex 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsCortexPol2MAdult8wksC57bl6StdSig\
type bigWig 0.110000 40.849998\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep2	Cortex 8wk Sg 2	bigWig 4.000000 65517.000000	Cortex Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	20	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Cortex 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=CORTEX localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqCortexCellPapMAdult8wksC57bl6SigRep2\
type bigWig 4.000000 65517.000000\

wgEncodePsuHistoneErythroblH3k36me3BE14halfCd1InputPk	Erythrob H3K36m3	broadPeak	Erythroblast H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	20	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Erythroblast H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Erythrob H3K36m3\
subGroups view=Peaks age=E14HALF factor=H3K36ME3 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k36me3BE14halfCd1InputPk\
type broadPeak\

phastConsElements30wayEuarch	Euarch El	bed 5 .	PhastCons Euarchontoglires Conserved Elements, 30-way Multiz Alignment	0	20	100	50	170	177	152	212	0	0	0				compGeno	1	color 100,50,170\
exonArrows off\
longLabel PhastCons Euarchontoglires Conserved Elements, 30-way Multiz Alignment\
noInherit on\
parent cons30wayViewelements on\
priority 20\
shortLabel Euarch El\
showTopScorers 200\
subGroups view=elements clade=glires\
track phastConsElements30wayEuarch\
type bed 5 .\

wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dPlusRawRep2	FV-progenitor P 2	bigWig 1.000000 1269997.000000	FV-progenitor 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	20	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel FV-progenitor 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel FV-progenitor P 2\
subGroups view=PlusRawSignal age=ADULT810WKS cellType=FVP readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dPlusRawRep2\
type bigWig 1.000000 1269997.000000\

wgEncodePsuTfbsG1eTal1ME0S129InputSig	G1E TAL1	bigWig 1.000000 326.000000	G1E TAL1 TFBS ChIP-seq Signal from ENCODE/PSU	2	20	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E TAL1 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal\
shortLabel G1E TAL1\
subGroups view=Signal age=E0 factor=TAL1 cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eTal1ME0S129InputSig\
type bigWig 1.000000 326.000000\
viewLimits 2:250\

wgEncodeSydhHistMelH3k04me3Dm2p5dIggyaleSig	MEL H3K4m3 DMSO Y	bigWig 1.000000 52086.000000	MEL H3K4me3 DMSO 2% IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	20	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K4me3 DMSO 2% IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig\
shortLabel MEL H3K4m3 DMSO Y\
subGroups view=Signal factor=H3K04ME3 cellType=MEL control=IGGYale treatment=DM2P5D\
track wgEncodeSydhHistMelH3k04me3Dm2p5dIggyaleSig\
type bigWig 1.000000 52086.000000\

wgEncodeFsuRepliChipEsem5sUDiffhsoxmWaveSignalRep2	Mesoderm Ws 2	bigWig -7.279305 2.019603	Mesoderm Gsc/Sox17- Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	20	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel Mesoderm Gsc/Sox17- Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel Mesoderm Ws 2\
subGroups view=WaveSignal cellType=ESEM5S sex=U treatment=DIFFHSOXM rep=rep2\
track wgEncodeFsuRepliChipEsem5sUDiffhsoxmWaveSignalRep2\
type bigWig -7.279305 2.019603\

wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep1	B_(CD43-) 8w A 1	bam	B-cell (CD43-) Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	21	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel B_(CD43-) 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=BCELLCD43N localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeLicrHistoneBatH3k04me1MAdult24wksC57bl6StdSig	BAT 24w H3K4m1	bigWig 0.130000 14.560000	Brown Adipose Tissue 24w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	21	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Brown Adipose Tissue 24w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BAT 24w H3K4m1\
subGroups view=Signal age=A2DULT24WKS factor=H3K04ME1 cellType=BAT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBatH3k04me1MAdult24wksC57bl6StdSig\
type bigWig 0.130000 14.560000\
viewLimits 0.2:3\

wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep1	Bcell (CD19+) S 1	bigWig 1.000000 84233.000000	B-cell (CD19+) DNaseI HS Signal Rep 1 from ENCODE/UW	2	21	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD19+) DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal\
shortLabel Bcell (CD19+) S 1\
subGroups view=Signal age=ADULT8WKS cellType=BCELLCD19P sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 84233.000000\

wgEncodeCaltechHistC2c12H3k36me3FCntrl50bE2p60hPcr1xPkRep1	C2 H3K36me3 60h 1	narrowPeak	C2C12 H3K36me3 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	21	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K36me3 Myocyte 60h Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks off\
shortLabel C2 H3K36me3 60h 1\
subGroups view=Peaks factor=H3K36ME3 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12H3k36me3FCntrl50bE2p60hPcr1xPkRep1\
type narrowPeak\

wgEncodeCaltechTfbsC2c12MaxFCntrl50bE2p60hPcr1xSigRep1	C2 Max 60h 1	bigWig 0.054500 12323.050781	C2C12 Max Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	21	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Max Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Max 60h 1\
subGroups view=Signal factor=MAX cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12MaxFCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.054500 12323.050781\

wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep2	Cerebellum - 2	bigWig 1.000000 586025.000000	Cerebellum A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	21	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Cerebellum - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=CBELLUM rep=rep2\
track wgEncodeCshlLongRnaSeqCbellumAdult8wksMinusRawRep2\
type bigWig 1.000000 586025.000000\

wgEncodeSydhTfbsCh12Mafkab50322IggrabPk	CH12 MafK_a	narrowPeak	CH12 MafK (ab50322) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	21	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 MafK (ab50322) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 MafK_a\
subGroups view=Peaks factor=MAFKAB50322 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Mafkab50322IggrabPk\
type narrowPeak\

wgEncodeFsuRepliChipEsem5sUDiffhsoxpWaveSignalRep1	Endoderm Ws 1	bigWig -2.805707 2.500815	Endoderm Gsc/Sox17+ Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	21	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel Endoderm Gsc/Sox17+ Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel Endoderm Ws 1\
subGroups view=WaveSignal cellType=ESEM5S sex=U treatment=DIFFHSOXP rep=rep1\
track wgEncodeFsuRepliChipEsem5sUDiffhsoxpWaveSignalRep1\
type bigWig -2.805707 2.500815\

wgEncodePsuHistoneErythroblH3k36me3BE14halfCd1InputSig	Erythrob H3K36m3	bigWig 1.000000 480.000000	Erythroblast H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	21	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Erythrob H3K36m3\
subGroups view=Signal age=E14HALF factor=H3K36ME3 cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblH3k36me3BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:500\

wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdPk	ES-B4 E0 CTCF	broadPeak	ES-Bruce4 Embryonic day 0 CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	21	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel ES-B4 E0 CTCF\
subGroups view=Peaks age=E0 factor=CTCF cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep1	ES-Bruce4 E0 Al 1	bam	ES-Bruce4 Embryonic day 0 RNA-seq Alignments Rep 1 from ENCODE/LICR	0	21	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel ES-Bruce4 E0 Al 1\
subGroups view=Alignments age=E0 cellType=ESB4 localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep1\
type bam\

wgEncodeUwDgfEscj7129s1ME0HotspotsRep1	ES-CJ7 E0 H	broadPeak	ES-CJ7 E0 129S1/SVImJ DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	21	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-CJ7 E0 129S1/SVImJ DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel ES-CJ7 E0 H\
subGroups view=Hotspots age=E0 cellType=ESCJ7 strain=A129S1 treatment=NONE rep=rep1\
track wgEncodeUwDgfEscj7129s1ME0HotspotsRep1\
type broadPeak\

wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dMinusRawRep2	FV-progenitor M 2	bigWig -641807.000000 -1.000000	FV-progenitor 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	21	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel FV-progenitor 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel FV-progenitor M 2\
subGroups view=MinusRawSignal age=ADULT810WKS cellType=FVP readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dMinusRawRep2\
type bigWig -641807.000000 -1.000000\

wgEncodePsuTfbsG1eInputME0S129InputSig	G1E Input	bigWig 1.000000 228.000000	G1E Input TFBS ChIP-seq Signal from ENCODE/PSU	2	21	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E Input TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E Input\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1E control=INPUT treatment=aNONE rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eInputME0S129InputSig\
type bigWig 1.000000 228.000000\

wgEncodeSydhHistMelH3k04me3IggrabSig	MEL H3K4m3 rab	bigWig 1.000000 22220.000000	MEL H3K4me3 IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	21	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K4me3 IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig\
shortLabel MEL H3K4m3 rab\
subGroups view=Signal factor=H3K04ME3 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhHistMelH3k04me3IggrabSig\
type bigWig 1.000000 22220.000000\

wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep2	B_(CD43-) 8w A 2	bam	B-cell (CD43-) Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW	0	22	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel B_(CD43-) 8w A 2\
subGroups view=Alignments age=ADULT8WKS cellType=BCELLCD43N localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeLicrHistoneBatH3k04me3MAdult24wksC57bl6StdPk	BAT 24w H3K4m3	broadPeak	Brown Adipose Tissue 24w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	22	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Brown Adipose Tissue 24w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BAT 24w H3K4m3\
subGroups view=Peaks age=A2DULT24WKS factor=H3K04ME3 cellType=BAT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBatH3k04me3MAdult24wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep2	Bcell (CD19+) H 2	broadPeak	B-cell (CD19+) DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	22	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD19+) DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Bcell (CD19+) H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=BCELLCD19P sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCaltechHistC2c12H3k36me3FCntrl50bE2p60hPcr1xSigRep1	C2 H3K36me3 60h 1	bigWig 0.044800 7791.657715	C2C12 H3K36me3 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	22	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3K36me3 Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 H3K36me3 60h 1\
subGroups view=Signal factor=H3K36ME3 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12H3k36me3FCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.044800 7791.657715\

wgEncodeCaltechTfbsC2c12MaxFCntrl50bPcr1xPkRep1	C2 Max Pk 1	narrowPeak	C2C12 Max Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	22	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Max Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 Max Pk 1\
subGroups view=Peaks factor=MAX cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12MaxFCntrl50bPcr1xPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep2	Cerebellum + 2	bigWig 1.000000 878213.000000	Cerebellum A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	22	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Cerebellum + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=CBELLUM rep=rep2\
track wgEncodeCshlLongRnaSeqCbellumAdult8wksPlusRawRep2\
type bigWig 1.000000 878213.000000\

wgEncodeSydhTfbsCh12Mafkab50322IggrabSig	CH12 MafK_a	bigWig 1.000000 211268.000000	CH12 MafK (ab50322) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	22	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 MafK (ab50322) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 MafK_a\
subGroups view=Signal factor=MAFKAB50322 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Mafkab50322IggrabSig\
type bigWig 1.000000 211268.000000\

wgEncodeFsuRepliChipEsem5sUDiffhsoxpWaveSignalRep2	Endoderm Ws 2	bigWig -11.218806 1.801808	Endoderm Gsc/Sox17+ Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	22	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel Endoderm Gsc/Sox17+ Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel Endoderm Ws 2\
subGroups view=WaveSignal cellType=ESEM5S sex=U treatment=DIFFHSOXP rep=rep2\
track wgEncodeFsuRepliChipEsem5sUDiffhsoxpWaveSignalRep2\
type bigWig -11.218806 1.801808\

wgEncodePsuHistoneErythroblInputBE14halfCd1InputSig	Erythrob Input	bigWig 1.000000 118.000000	Erythroblast Input Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	22	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Erythroblast Input Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel Erythrob Input\
subGroups view=Signal age=E14HALF factor=zINPUT cellType=ERYTHROBL control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneErythroblInputBE14halfCd1InputSig\
type bigWig 1.000000 118.000000\

wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdSig	ES-B4 E0 CTCF	bigWig 0.110000 65.250000	ES-Bruce4 Embryonic day 0 CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	22	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel ES-B4 E0 CTCF\
subGroups view=Signal age=E0 factor=CTCF cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsEsb4CtcfME0C57bl6StdSig\
type bigWig 0.110000 65.250000\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep2	ES-Bruce4 E0 Al 2	bam	ES-Bruce4 Embryonic day 0 RNA-seq Alignments Rep 2 from ENCODE/LICR	0	22	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel ES-Bruce4 E0 Al 2\
subGroups view=Alignments age=E0 cellType=ESB4 localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6AlnRep2\
type bam\

wgEncodeUwDgfEscj7129s1ME0PkRep1	ES-CJ7 E0 P	narrowPeak	ES-CJ7 E0 129S1/SVImJ DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	22	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-CJ7 E0 129S1/SVImJ DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel ES-CJ7 E0 P\
subGroups view=Peaks age=E0 cellType=ESCJ7 strain=A129S1 treatment=NONE rep=rep1\
track wgEncodeUwDgfEscj7129s1ME0PkRep1\
type narrowPeak\

wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dAlnRep2	FV-progenitor A 2	bam	FV-progenitor 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU	0	22	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel FV-progenitor 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel FV-progenitor A 2\
subGroups view=Alignments age=ADULT810WKS cellType=FVP readType=R2X99D sex=B strain=BALBCJ treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqFvpBAdult810wksBalbcjR2x99dAlnRep2\
type bam\

wgEncodePsuTfbsG1eer4e2CtcfME0S129InputPk	G1E-ER CTCF 24hr	broadPeak	G1E-ER4 CTCF Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU	3	22	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 CTCF Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E-ER CTCF 24hr\
subGroups view=Peaks age=E0 factor=CTCF cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2CtcfME0S129InputPk\
type broadPeak\

phastConsElements30wayPlacental	Mammal El	bed 5 .	PhastCons Placental Mammal Conserved Elements, 30-way Multiz Alignment	0	22	100	50	170	177	152	212	0	0	0				compGeno	1	color 100,50,170\
exonArrows off\
longLabel PhastCons Placental Mammal Conserved Elements, 30-way Multiz Alignment\
noInherit on\
parent cons30wayViewelements off\
priority 22\
shortLabel Mammal El\
showTopScorers 200\
subGroups view=elements clade=mammal\
track phastConsElements30wayPlacental\
type bed 5 .\

wgEncodeSydhHistMelH3k4me3IggyaleSig	MEL H3K4m3 Y	bigWig 1 38729	MEL H3K4me3 IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	22	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K4me3 IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig\
shortLabel MEL H3K4m3 Y\
subGroups view=Signal factor=H3K04ME3 cellType=MEL control=IGGYale treatment=zNONE\
track wgEncodeSydhHistMelH3k4me3IggyaleSig\
type bigWig 1 38729\

wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep1	B_(CD43-) 8w MR 1	bigWig 1.000000 130053.000000	B-cell (CD43-) Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	23	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel B_(CD43-) 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=BCELLCD43N localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 130053.000000\

wgEncodeLicrHistoneBatH3k04me3MAdult24wksC57bl6StdSig	BAT 24w H3K4m3	bigWig 0.160000 60.709999	Brown Adipose Tissue 24w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	23	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Brown Adipose Tissue 24w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BAT 24w H3K4m3\
subGroups view=Signal age=A2DULT24WKS factor=H3K04ME3 cellType=BAT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBatH3k04me3MAdult24wksC57bl6StdSig\
type bigWig 0.160000 60.709999\
viewLimits 0.2:10\

wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep2	Bcell (CD19+) P 2	narrowPeak	B-cell (CD19+) DNaseI HS Peaks Rep 2 from ENCODE/UW	3	23	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD19+) DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Bcell (CD19+) P 2\
subGroups view=Peaks age=ADULT8WKS cellType=BCELLCD19P sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeCaltechHistC2c12H3k36me3FCntrl50bPcr1xPkRep1	C2 H3K36me3 1	narrowPeak	C2C12 H3K36me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	23	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 H3K36me3 Myoblast Hist Mods ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewPeaks off\
shortLabel C2 H3K36me3 1\
subGroups view=Peaks factor=H3K36ME3 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12H3k36me3FCntrl50bPcr1xPkRep1\
type narrowPeak\

wgEncodeCaltechTfbsC2c12MaxFCntrl50bPcr1xSigRep1	C2 Max 1	bigWig 0.038000 10295.183594	C2C12 Max Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	23	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Max Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Max 1\
subGroups view=Signal factor=MAX cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12MaxFCntrl50bPcr1xSigRep1\
type bigWig 0.038000 10295.183594\

wgEncodeCshlLongRnaSeqCbellumAdult8wksContigs	Cerebellum C	bed 6 +	Cerebellum A8 Long RNA-seq Contigs from ENCODE/CSHL	3	23	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Cerebellum C\
subGroups view=Contigs age=ADULT8WKS cellType=CBELLUM rep=repP\
track wgEncodeCshlLongRnaSeqCbellumAdult8wksContigs\
type bed 6 +\

wgEncodeSydhTfbsCh12MaxIggrabPk	CH12 Max	narrowPeak	CH12 Max TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	23	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 Max TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 Max\
subGroups view=Peaks factor=MAX cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12MaxIggrabPk\
type narrowPeak\

wgEncodeLicrTfbsEsb4InputME0C57bl6StdSig	ES-B4 E0 Input	bigWig 0.130000 64.720001	ES-Bruce4 Embryonic day 0 Input TFBS ChIP-seq Signal from ENCODE/LICR	2	23	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel ES-B4 E0 Input\
subGroups view=Signal age=E0 factor=INPUT cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsEsb4InputME0C57bl6StdSig\
type bigWig 0.130000 64.720001\

wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep1	ES-Bruce4 E0 Sg 1	bigWig 0.000000 65475.000000	ES-Bruce4 Embryonic day 0 RNA-seq Signal Rep 1 from ENCODE/LICR	2	23	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel ES-Bruce4 E0 Sg 1\
subGroups view=Signal age=E0 cellType=ESB4 localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep1\
type bigWig 0.000000 65475.000000\

wgEncodeUwDgfEscj7129s1ME0RawRep1	ES-CJ7 E0 R	bigWig 1.000000 425541.000000	ES-CJ7 E0 129S1/SVImJ DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	23	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-CJ7 E0 129S1/SVImJ DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel ES-CJ7 E0 R\
subGroups view=RawSignal age=E0 cellType=ESCJ7 strain=A129S1 treatment=NONE rep=rep1\
track wgEncodeUwDgfEscj7129s1ME0RawRep1\
type bigWig 1.000000 425541.000000\

wgEncodeFsuRepliChipEstt2MDifff9dWaveSignalRep1	ES-TT2 NP Ws 1	bigWig -5.522534 2.160326	ES-TT2 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	23	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-TT2 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-TT2 NP Ws 1\
subGroups view=WaveSignal cellType=ESTT2 sex=M treatment=DIFFF9D rep=rep1\
track wgEncodeFsuRepliChipEstt2MDifff9dWaveSignalRep1\
type bigWig -5.522534 2.160326\

wgEncodePsuHistoneG1eH3k04me1ME0S129InputPk	G1E H3K4m1	broadPeak	G1E H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	23	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E H3K4m1\
subGroups view=Peaks age=E0 factor=H3K04ME1 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k04me1ME0S129InputPk\
type broadPeak\

wgEncodePsuRnaSeqG1eME0S129R1x36SigRep1	G1E S 1	bigWig 1.000000 48059.000000	G1E single read (1x36) RNA-seq Signal Rep 1 from ENCODE/PSU	2	23	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E single read (1x36) RNA-seq Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal off\
shortLabel G1E S 1\
subGroups view=Signal age=E0 cellType=G1E readType=R1X36 sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqG1eME0S129R1x36SigRep1\
type bigWig 1.000000 48059.000000\

wgEncodePsuTfbsG1eer4e2CtcfME0S129InputSig	G1E-ER CTCF 24hr	bigWig 1.000000 244.000000	G1E-ER4 CTCF Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU	2	23	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 CTCF Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER CTCF 24hr\
subGroups view=Signal age=E0 factor=CTCF cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2CtcfME0S129InputSig\
type bigWig 1.000000 244.000000\
viewLimits 1:100\

wgEncodeSydhHistMelH3k09me3Dm2p5dStdPk	MEL H3K9m3 DMSO	narrowPeak	MEL H3K9me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	23	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K9me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks off\
shortLabel MEL H3K9m3 DMSO\
subGroups view=Peaks factor=H3K09ME3 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k09me3Dm2p5dStdPk\
type narrowPeak\

phastConsElements30way	Vertebrate El	bed 5 .	PhastCons Vertebrate Conserved Elements, 30-way Multiz Alignment	0	23	170	100	50	212	177	152	0	0	0				compGeno	1	color 170,100,50\
exonArrows off\
longLabel PhastCons Vertebrate Conserved Elements, 30-way Multiz Alignment\
noInherit on\
parent cons30wayViewelements off\
priority 23\
shortLabel Vertebrate El\
showTopScorers 200\
subGroups view=elements clade=vert\
track phastConsElements30way\
type bed 5 .\

wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep2	B_(CD43-) MR 2	bigWig 1.000000 60848.000000	B-cell (CD43-) Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	24	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel B_(CD43-) MR 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=BCELLCD43N localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6MinusRawRep2\
type bigWig 1.000000 60848.000000\

wgEncodeLicrHistoneBatH3k27acMAdult24wksC57bl6StdPk	BAT 24w H3K27a	broadPeak	Brown Adipose Tissue 24w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	24	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Brown Adipose Tissue 24w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel BAT 24w H3K27a\
subGroups view=Peaks age=A2DULT24WKS factor=H3K27AC cellType=BAT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBatH3k27acMAdult24wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep2	Bcell (CD19+) S 2	bigWig 1.000000 159668.000000	B-cell (CD19+) DNaseI HS Signal Rep 2 from ENCODE/UW	2	24	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD19+) DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Bcell (CD19+) S 2\
subGroups view=Signal age=ADULT8WKS cellType=BCELLCD19P sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseBcellcd19pC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 159668.000000\

wgEncodeCaltechHistC2c12H3k36me3FCntrl50bPcr1xSigRep1	C2 H3K36me3 1	bigWig 0.027400 8452.805664	C2C12 H3K36me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	24	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 H3K36me3 Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 H3K36me3 1\
subGroups view=Signal factor=H3K36ME3 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12H3k36me3FCntrl50bPcr1xSigRep1\
type bigWig 0.027400 8452.805664\

wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xPkRep1	C2 NRSF 60h 1	narrowPeak	C2C12 NRSF Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	24	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 NRSF Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 NRSF 60h 1\
subGroups view=Peaks factor=NRSF cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqCbellumAdult8wksJunctions	Cerebellum J	bed 6 +	Cerebellum A8 Long RNA-seq Junctions from ENCODE/CSHL	0	24	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Cerebellum J\
subGroups view=SJunctions age=ADULT8WKS cellType=CBELLUM rep=repP\
track wgEncodeCshlLongRnaSeqCbellumAdult8wksJunctions\
type bed 6 +\

wgEncodeSydhTfbsCh12MaxIggrabSig	CH12 Max	bigWig 1.000000 122997.000000	CH12 Max TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	24	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Max TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 Max\
subGroups view=Signal factor=MAX cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12MaxIggrabSig\
type bigWig 1.000000 122997.000000\

wgEncodeLicrTfbsEsb4P300ME0C57bl6StdPk	ES-B4 E0 p300	broadPeak	ES-Bruce4 Embryonic day 0 p300 TFBS ChIP-seq Peaks from ENCODE/LICR	3	24	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 p300 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel ES-B4 E0 p300\
subGroups view=Peaks age=E0 factor=P300 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsEsb4P300ME0C57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep2	ES-Bruce4 E0 Sg 2	bigWig 0.000000 65447.000000	ES-Bruce4 Embryonic day 0 RNA-seq Signal Rep 2 from ENCODE/LICR	2	24	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel ES-Bruce4 E0 Sg 2\
subGroups view=Signal age=E0 cellType=ESB4 localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqEsb4CellPapME0C57bl6SigRep2\
type bigWig 0.000000 65447.000000\

wgEncodeUwDgfEscj7129s1ME0SigRep1	ES-CJ7 E0 S	bigWig 1.000000 79700.000000	ES-CJ7 E0 129S1/SVImJ DNaseI DGF Signal Rep 1 from ENCODE/UW	2	24	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-CJ7 E0 129S1/SVImJ DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel ES-CJ7 E0 S\
subGroups view=Signal age=E0 cellType=ESCJ7 strain=A129S1 treatment=NONE rep=rep1\
track wgEncodeUwDgfEscj7129s1ME0SigRep1\
type bigWig 1.000000 79700.000000\

wgEncodeFsuRepliChipEstt2MDifff9dWaveSignalRep2	ES-TT2 NP Ws 2	bigWig -13.130930 2.447524	ES-TT2 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	24	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-TT2 NP 9 d Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-TT2 NP Ws 2\
subGroups view=WaveSignal cellType=ESTT2 sex=M treatment=DIFFF9D rep=rep2\
track wgEncodeFsuRepliChipEstt2MDifff9dWaveSignalRep2\
type bigWig -13.130930 2.447524\

wgEncodePsuRnaSeqG1eME0S129R1x36AlnRep1	G1E A 1	bam	G1E single read (1x36) RNA-seq Alignments Rep 1 from ENCODE/PSU	0	24	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E single read (1x36) RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E A 1\
subGroups view=Alignments age=E0 cellType=G1E readType=R1X36 sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqG1eME0S129R1x36AlnRep1\
type bam\

wgEncodePsuHistoneG1eH3k04me1ME0S129InputSig	G1E H3K4m1	bigWig 1.000000 479.000000	G1E H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	24	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E H3K4m1\
subGroups view=Signal age=E0 factor=H3K04ME1 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k04me1ME0S129InputSig\
type bigWig 1.000000 479.000000\
viewLimits 2:150\

wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputPk	G1E-ER GATA1 24hr	broadPeak	G1E-ER4 GATA1 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU	3	24	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks\
shortLabel G1E-ER GATA1 24hr\
subGroups view=Peaks age=E0 factor=GATA1a cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputPk\
type broadPeak\

wgEncodeSydhHistMelH3k09me3IggrabPk	MEL H3K9m3 rab	narrowPeak	MEL H3K9me3 IgG-rab Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	24	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K9me3 IgG-rab Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks off\
shortLabel MEL H3K9m3 rab\
subGroups view=Peaks factor=H3K09ME3 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhHistMelH3k09me3IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep1	B_(CD43-) 8w PR 1	bigWig 1.000000 129927.000000	B-cell (CD43-) Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	25	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel B_(CD43-) 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=BCELLCD43N localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 129927.000000\

wgEncodeLicrHistoneBatH3k27acMAdult24wksC57bl6StdSig	BAT 24w H3K27a	bigWig 0.110000 46.150002	Brown Adipose Tissue 24w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	25	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Brown Adipose Tissue 24w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BAT 24w H3K27a\
subGroups view=Signal age=A2DULT24WKS factor=H3K27AC cellType=BAT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBatH3k27acMAdult24wksC57bl6StdSig\
type bigWig 0.110000 46.150002\
viewLimits 0.2:5\

wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep1	Bcell (CD43-) H 1	broadPeak	B-cell (CD43-) DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	25	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Bcell (CD43-) H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=BCELLCD43N sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCaltechHistC2c12InputFCntrl32bE2p24hPcr2xSigRep1	C2 Con 32bp 24h 1	bigWig 0.086100 1009.830200	C2C12 Contr 32bp Myocyte 24h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	25	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Contr 32bp Myocyte 24h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 Con 32bp 24h 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechHistC2c12InputFCntrl32bE2p24hPcr2xSigRep1\
type bigWig 0.086100 1009.830200\

wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xSigRep1	C2 NRSF 60h 1	bigWig 0.087400 1262.788086	C2C12 NRSF Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	25	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 NRSF Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 NRSF 60h 1\
subGroups view=Signal factor=NRSF cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12NrsfFCntrl32bE2p60hPcr2xSigRep1\
type bigWig 0.087400 1262.788086\

wgEncodeSydhTfbsCh12Mazab85725IggrabPk	CH12 MAZ P	narrowPeak	CH12 MAZ (ab85725) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	25	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 MAZ (ab85725) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 MAZ P\
subGroups view=Peaks factor=MAZAB85725 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Mazab85725IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE11halfAlnRep1	CNS E11.5 Aln 1	bam	CNS E11.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	25	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E11.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel CNS E11.5 Aln 1\
subGroups view=Alignments age=E11HALF cellType=CNS rep=rep1\
track wgEncodeCshlLongRnaSeqCnsE11halfAlnRep1\
type bam\

wgEncodeLicrTfbsEsb4P300ME0C57bl6StdSig	ES-B4 E0 p300	bigWig 0.140000 73.150002	ES-Bruce4 Embryonic day 0 p300 TFBS ChIP-seq Signal from ENCODE/LICR	2	25	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 p300 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel ES-B4 E0 p300\
subGroups view=Signal age=E0 factor=P300 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsEsb4P300ME0C57bl6StdSig\
type bigWig 0.140000 73.150002\
viewLimits 0.2:3\

wgEncodeFsuRepliChipEstt2MWaveSignalRep1	ES-TT2 Ws 1	bigWig -10.300041 2.263489	ES-TT2 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	25	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-TT2 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-TT2 Ws 1\
subGroups view=WaveSignal cellType=ESTT2 sex=M treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipEstt2MWaveSignalRep1\
type bigWig -10.300041 2.263489\

wgEncodePsuHistoneG1eH3k04me3ME0S129InputPk	G1E H3K4m3	broadPeak	G1E H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	25	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E H3K4m3\
subGroups view=Peaks age=E0 factor=H3K04ME3 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k04me3ME0S129InputPk\
type broadPeak\

wgEncodePsuRnaSeqG1eME0S129R1x55SigRep2	G1E S 2	bigWig 1.000000 272937.000000	G1E single read (1x55) RNA-seq Signal Rep 2 from ENCODE/PSU	2	25	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E single read (1x55) RNA-seq Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal off\
shortLabel G1E S 2\
subGroups view=Signal age=E0 cellType=G1E readType=R1X55 sex=M strain=s129 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqG1eME0S129R1x55SigRep2\
type bigWig 1.000000 272937.000000\

wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputSig	G1E-ER GATA1 24hr	bigWig 1.000000 212.000000	G1E-ER4 GATA1 Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU	2	25	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal\
shortLabel G1E-ER GATA1 24hr\
subGroups view=Signal age=E0 factor=GATA1a cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2Gata1aME0S129InputSig\
type bigWig 1.000000 212.000000\
viewLimits 2:150\

wgEncodeUwDgfHeartC57bl6MAdult8wksHotspotsRep1	Heart 8w H	broadPeak	Heart 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	25	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots\
shortLabel Heart 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=HEART strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfHeartC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep1	Heart 8wk Al 1	bam	Heart Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	25	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Heart 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=HEART localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeSydhHistMelH3k09me3Dm2p5dStdSig	MEL H3K9m3 DMSO	bigWig 1.000000 131256.000000	MEL H3K9me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	25	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K9me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel MEL H3K9m3 DMSO\
subGroups view=Signal factor=H3K09ME3 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k09me3Dm2p5dStdSig\
type bigWig 1.000000 131256.000000\

wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep2	B_(CD43-) 8w PR 2	bigWig 1.000000 60777.000000	B-cell (CD43-) Adult 8 weeks RNA-seq Plus Raw signal Rep 2 from ENCODE/UW	2	26	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) Adult 8 weeks RNA-seq Plus Raw signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel B_(CD43-) 8w PR 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=BCELLCD43N localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6PlusRawRep2\
type bigWig 1.000000 60777.000000\

wgEncodeLicrHistoneBatInputMAdult24wksC57bl6StdSig	BAT 24w Input	bigWig 0.100000 50.900002	Brown Adipose Tissue 24w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	26	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Brown Adipose Tissue 24w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel BAT 24w Input\
subGroups view=Signal age=A2DULT24WKS factor=INPUT cellType=BAT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneBatInputMAdult24wksC57bl6StdSig\
type bigWig 0.100000 50.900002\
viewLimits 0.2:5\

wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep1	Bcell (CD43-) P 1	narrowPeak	B-cell (CD43-) DNaseI HS Peaks Rep 1 from ENCODE/UW	3	26	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Bcell (CD43-) P 1\
subGroups view=Peaks age=ADULT8WKS cellType=BCELLCD43N sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCaltechHistC2c12InputFCntrl32bE2p60hPcr2xSigRep1	C2 Con 32bp 60h 1	bigWig 0.042600 2602.975830	C2C12 Contr 32bp Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	26	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Contr 32bp Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 Con 32bp 60h 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12InputFCntrl32bE2p60hPcr2xSigRep1\
type bigWig 0.042600 2602.975830\

wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xPkRep1	C2 Pol2 60h 1	narrowPeak	C2C12 Pol2 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	26	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Pol2 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 Pol2 60h 1\
subGroups view=Peaks factor=POL2 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xPkRep1\
type narrowPeak\

wgEncodeSydhTfbsCh12Mazab85725IggrabSig	CH12 MAZ S	bigWig 1.000000 106499.000000	CH12 MAZ (ab85725) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	26	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 MAZ (ab85725) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 MAZ S\
subGroups view=Signal factor=MAZAB85725 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Mazab85725IggrabSig\
type bigWig 1.000000 106499.000000\

wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep1	CNS E11.5 - 1	bigWig 1.000000 1135308.000000	CNS E11.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	26	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E11.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel CNS E11.5 - 1\
subGroups view=MinusRawSignal age=E11HALF cellType=CNS rep=rep1\
track wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep1\
type bigWig 1.000000 1135308.000000\

wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdPk	ES-B4 E0 Pol2	broadPeak	ES-Bruce4 Embryonic day 0 Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	26	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel ES-B4 E0 Pol2\
subGroups view=Peaks age=E0 factor=POL2 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdPk\
type broadPeak\

wgEncodeFsuRepliChipEstt2MWaveSignalRep2	ES-TT2 Ws 2	bigWig -4.597528 2.123765	ES-TT2 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	26	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-TT2 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel ES-TT2 Ws 2\
subGroups view=WaveSignal cellType=ESTT2 sex=M treatment=NONE rep=rep2\
track wgEncodeFsuRepliChipEstt2MWaveSignalRep2\
type bigWig -4.597528 2.123765\

wgEncodePsuRnaSeqG1eME0S129R1x55AlnRep2	G1E A 2	bam	G1E single read (1x55) RNA-seq Alignments Rep 2 from ENCODE/PSU	0	26	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E single read (1x55) RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E A 2\
subGroups view=Alignments age=E0 cellType=G1E readType=R1X55 sex=M strain=s129 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqG1eME0S129R1x55AlnRep2\
type bam\

wgEncodePsuHistoneG1eH3k04me3ME0S129InputSig	G1E H3K4m3	bigWig 1.000000 480.000000	G1E H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	26	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E H3K4m3\
subGroups view=Signal age=E0 factor=H3K04ME3 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k04me3ME0S129InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:450\

wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputPk	G1E-ER GATA2 24hr	broadPeak	G1E-ER4 GATA2 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU	3	26	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 GATA2 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E-ER GATA2 24hr\
subGroups view=Peaks age=E0 factor=GATA2SC9008 cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputPk\
type broadPeak\

wgEncodeUwDgfHeartC57bl6MAdult8wksPkRep1	Heart 8w P	narrowPeak	Heart 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	26	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks\
shortLabel Heart 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=HEART strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfHeartC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep2	Heart 8wk Al 2	bam	Heart Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	26	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Heart 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=HEART localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeSydhHistMelH3k09me3IggrabSig	MEL H3K9m3 rab	bigWig 1.000000 158172.000000	MEL H3K9me3 IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	26	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K9me3 IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel MEL H3K9m3 rab\
subGroups view=Signal factor=H3K09ME3 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhHistMelH3k09me3IggrabSig\
type bigWig 1.000000 158172.000000\

wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep1	B_(CD43-) 8w S 1	bigWig 1.000000 130092.000000	B-cell (CD43-) Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	27	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel B_(CD43-) 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=BCELLCD43N localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 130092.000000\

wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep1	Bcell (CD43-) S 1	bigWig 1.000000 45976.000000	B-cell (CD43-) DNaseI HS Signal Rep 1 from ENCODE/UW	2	27	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Bcell (CD43-) S 1\
subGroups view=Signal age=ADULT8WKS cellType=BCELLCD43N sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 45976.000000\

wgEncodeCaltechHistC2c12InputFCntrl32bPcr2xSigRep1	C2 Con 32bp 1	bigWig 0.077700 1187.887817	C2C12 Contr 32bp Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	27	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Contr 32bp Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 Con 32bp 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12InputFCntrl32bPcr2xSigRep1\
type bigWig 0.077700 1187.887817\

wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xSigRep1	C2 Pol2 60h 1	bigWig 0.060300 133.534302	C2C12 Pol2 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	27	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Pol2 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Pol2 60h 1\
subGroups view=Signal factor=POL2 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Pol2FCntrl32bE2p60hPcr2xSigRep1\
type bigWig 0.060300 133.534302\

wgEncodeLicrHistoneCbellumH3k4me1MAdult8wksC57bl6StdPk	Cbellum H3K4m1	broadPeak	Cerebellum 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	27	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Cbellum H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCbellumH3k4me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsCh12Mxi1af4185IggrabPk	CH12 Mxi1	narrowPeak	CH12 Mxi1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	27	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 Mxi1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 Mxi1\
subGroups view=Peaks factor=MXI1AF4185 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Mxi1af4185IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep1	CNS E11.5 + 1	bigWig 1.000000 1047677.000000	CNS E11.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	27	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E11.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel CNS E11.5 + 1\
subGroups view=PlusRawSignal age=E11HALF cellType=CNS rep=rep1\
track wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep1\
type bigWig 1.000000 1047677.000000\

wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdSig	ES-B4 E0 Pol2	bigWig 0.130000 73.010002	ES-Bruce4 Embryonic day 0 Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	27	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 Embryonic day 0 Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel ES-B4 E0 Pol2\
subGroups view=Signal age=E0 factor=POL2 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsEsb4Pol2ME0C57bl6StdSig\
type bigWig 0.130000 73.010002\
viewLimits 0.2:3\

wgEncodePsuHistoneG1eH3k09me3ME0S129InputPk	G1E H3K9m3	broadPeak	G1E H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	27	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E H3K9m3\
subGroups view=Peaks age=E0 factor=H3K09ME3 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k09me3ME0S129InputPk\
type broadPeak\

wgEncodePsuRnaSeqG1eME0S129R2x99dPlusRawRep1	G1E P 1	bigWig 1.000000 1696370.000000	G1E 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	27	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal\
shortLabel G1E P 1\
subGroups view=PlusRawSignal age=E0 cellType=G1E readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqG1eME0S129R2x99dPlusRawRep1\
type bigWig 1.000000 1696370.000000\

wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputSig	G1E-ER GATA2 24hr	bigWig 1.000000 98.000000	G1E-ER4 GATA2 Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU	2	27	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 GATA2 Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER GATA2 24hr\
subGroups view=Signal age=E0 factor=GATA2SC9008 cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2Gata2sc9008ME0S129InputSig\
type bigWig 1.000000 98.000000\
viewLimits 2:20\

wgEncodeUwDgfHeartC57bl6MAdult8wksRawRep1	Heart 8w R	bigWig 1.000000 379588.000000	Heart 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	27	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal\
shortLabel Heart 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=HEART strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfHeartC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 379588.000000\

wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep1	Heart E14.5 Al 1	bam	Heart Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR	0	27	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Heart E14.5 Al 1\
subGroups view=Alignments age=E14HALF cellType=HEART localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep1\
type bam\

wgEncodeFsuRepliChipJ185aUWaveSignalRep1	J185a Ws 1	bigWig -2.900778 4.882994	J185a Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	27	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel J185a Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel J185a Ws 1\
subGroups view=WaveSignal cellType=J185A sex=U treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipJ185aUWaveSignalRep1\
type bigWig -2.900778 4.882994\

wgEncodeSydhHistMelH3k27me3bDm2p5dStdPk	MEL H3K27m3 DMSO	narrowPeak	MEL H3K27me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	27	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K27me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks off\
shortLabel MEL H3K27m3 DMSO\
subGroups view=Peaks factor=H3K27ME3b cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k27me3bDm2p5dStdPk\
type narrowPeak\

wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep2	B_(CD43-) 8w S 2	bigWig 1.000000 60860.000000	B-cell (CD43-) Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW	2	28	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel B_(CD43-) 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=BCELLCD43N localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqBcellcd43nCellPolyaMAdult8wksC57bl6SigRep2\
type bigWig 1.000000 60860.000000\

wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep2	Bcell (CD43-) H 2	broadPeak	B-cell (CD43-) DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	28	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Bcell (CD43-) H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=BCELLCD43N sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCaltechHistC2c12InputFCntrl50bE2p60hPcr1xSigRep1	C2 Con 50bp 60h 1	bigWig 0.052000 10580.088867	C2C12 Contr 50bp Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	28	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Contr 50bp Myocyte 60h Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 Con 50bp 60h 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechHistC2c12InputFCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.052000 10580.088867\

wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xPkRep1	C2 Pol2S2 60h 1	narrowPeak	C2C12 Pol2S2 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	28	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Pol2S2 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 Pol2S2 60h 1\
subGroups view=Peaks factor=POL2S2 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xPkRep1\
type narrowPeak\

wgEncodeLicrHistoneCbellumH3k4me1MAdult8wksC57bl6StdSig	Cbellum H3K4m1	bigWig 0.120000 18.879999	Cerebellum 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	28	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Cbellum H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCbellumH3k4me1MAdult8wksC57bl6StdSig\
type bigWig 0.120000 18.879999\
viewLimits 0.2:3\

wgEncodeSydhTfbsCh12Mxi1af4185IggrabSig	CH12 Mxi1	bigWig 1.000000 122280.000000	CH12 Mxi1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	28	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Mxi1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 Mxi1\
subGroups view=Signal factor=MXI1AF4185 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Mxi1af4185IggrabSig\
type bigWig 1.000000 122280.000000\

wgEncodeCshlLongRnaSeqCnsE11halfAlnRep2	CNS E11.5 Aln 2	bam	CNS E11.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	28	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E11.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel CNS E11.5 Aln 2\
subGroups view=Alignments age=E11HALF cellType=CNS rep=rep2\
track wgEncodeCshlLongRnaSeqCnsE11halfAlnRep2\
type bam\

wgEncodePsuHistoneG1eH3k09me3ME0S129InputSig	G1E H3K9m3	bigWig 1.000000 480.000000	G1E H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	28	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E H3K9m3\
subGroups view=Signal age=E0 factor=H3K09ME3 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k09me3ME0S129InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:100\

wgEncodePsuRnaSeqG1eME0S129R2x99dMinusRawRep1	G1E M 1	bigWig -3176578.000000 -1.000000	G1E 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	28	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal\
shortLabel G1E M 1\
subGroups view=MinusRawSignal age=E0 cellType=G1E readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqG1eME0S129R2x99dMinusRawRep1\
type bigWig -3176578.000000 -1.000000\

wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputPk	G1E-ER Pol2 24hr	broadPeak	G1E-ER4 Pol2-4H8 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU	3	28	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Pol2-4H8 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E-ER Pol2 24hr\
subGroups view=Peaks age=E0 factor=POL24H8 cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputPk\
type broadPeak\

wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdPk	Heart 8w CTCF	broadPeak	Heart Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	28	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks\
shortLabel Heart 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDgfHeartC57bl6MAdult8wksSigRep1	Heart 8w S	bigWig 1.000000 75815.000000	Heart 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	28	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal\
shortLabel Heart 8w S\
subGroups view=Signal age=ADULT8WKS cellType=HEART strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfHeartC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 75815.000000\

wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep2	Heart E14.5 Al 2	bam	Heart Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR	0	28	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Heart E14.5 Al 2\
subGroups view=Alignments age=E14HALF cellType=HEART localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6AlnRep2\
type bam\

wgEncodeFsuRepliChipJ185aUWaveSignalRep2	J185a Ws 2	bigWig -6.760349 2.574383	J185a Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	28	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel J185a Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel J185a Ws 2\
subGroups view=WaveSignal cellType=J185A sex=U treatment=NONE rep=rep2\
track wgEncodeFsuRepliChipJ185aUWaveSignalRep2\
type bigWig -6.760349 2.574383\

wgEncodeSydhHistMelH3k27me3bDm2p5dStdSig	MEL H3K27m3 DMSO	bigWig 1.000000 46121.000000	MEL H3K27me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	28	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K27me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel MEL H3K27m3 DMSO\
subGroups view=Signal factor=H3K27ME3b cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k27me3bDm2p5dStdSig\
type bigWig 1.000000 46121.000000\

wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep2	Bcell (CD43-) P 2	narrowPeak	B-cell (CD43-) DNaseI HS Peaks Rep 2 from ENCODE/UW	3	29	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel B-cell (CD43-) DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Bcell (CD43-) P 2\
subGroups view=Peaks age=ADULT8WKS cellType=BCELLCD43N sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeCaltechHistC2c12InputFCntrl50bPcr1xSigRep1	C2 Con 50bp 1	bigWig 0.073500 10874.264648	C2C12 Contr 50bp Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	29	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Contr 50bp Myoblast Hist Mods ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechHistViewSignal off\
shortLabel C2 Con 50bp 1\
subGroups view=Signal factor=INPUT cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechHistC2c12InputFCntrl50bPcr1xSigRep1\
type bigWig 0.073500 10874.264648\

wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xSigRep1	C2 Pol2S2 60h 1	bigWig 0.049700 139.236496	C2C12 Pol2S2 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	29	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Pol2S2 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Pol2S2 60h 1\
subGroups view=Signal factor=POL2S2 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Pol2s2FCntrl32bE2p60hPcr2xSigRep1\
type bigWig 0.049700 139.236496\

wgEncodeLicrHistoneCbellumH3k4me3MAdult8wksC57bl6StdPk	Cbellum H3K4m3	broadPeak	Cerebellum 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	29	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Cbellum H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCbellumH3k4me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsCh12NelfeIggrabPk	CH12 NELFe	narrowPeak	CH12 NELFe TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	29	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 NELFe TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 NELFe\
subGroups view=Peaks factor=NELFE cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12NelfeIggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep2	CNS E11.5 - 2	bigWig 1.000000 330563.000000	CNS E11.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	29	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E11.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel CNS E11.5 - 2\
subGroups view=MinusRawSignal age=E11HALF cellType=CNS rep=rep2\
track wgEncodeCshlLongRnaSeqCnsE11halfMinusRawRep2\
type bigWig 1.000000 330563.000000\

wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep1	Crbellum 8w A 1	bam	Cerebellum Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	29	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Crbellum 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodePsuRnaSeqG1eME0S129R2x99dAlnRep1	G1E A 1	bam	G1E 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU	0	29	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E A 1\
subGroups view=Alignments age=E0 cellType=G1E readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqG1eME0S129R2x99dAlnRep1\
type bam\

wgEncodePsuHistoneG1eH3k27me3ME0S129InputPk	G1E H3K27m3	broadPeak	G1E H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	29	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E H3K27m3\
subGroups view=Peaks age=E0 factor=H3K27ME3 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k27me3ME0S129InputPk\
type broadPeak\

wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputSig	G1E-ER Pol2 24hr	bigWig 1.000000 358.000000	G1E-ER4 Pol2-4H8 2hr Estradiol TFBS ChIP-seq Signal from ENCODE/PSU	2	29	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Pol2-4H8 2hr Estradiol TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER Pol2 24hr\
subGroups view=Signal age=E0 factor=POL24H8 cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2Pol24h8ME0S129InputSig\
type bigWig 1.000000 358.000000\
viewLimits 5:50\

wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdSig	Heart 8w CTCF	bigWig 0.120000 52.910000	Heart Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	29	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal\
shortLabel Heart 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsHeartCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.120000 52.910000\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep1	Heart 8wk Sg 1	bigWig 4.000000 65485.000000	Heart Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	29	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel Heart 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=HEART localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep1\
type bigWig 4.000000 65485.000000\

wgEncodeUwDgfKidneyC57bl6MAdult8wksHotspotsRep1	Kidney 8w H	broadPeak	Kidney 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	29	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel Kidney 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=KIDNEY strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfKidneyC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeFsuRepliChipL1210FWaveSignalRep1	L1210 Ws 1	bigWig -17.782591 5.268431	L1210 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	29	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel L1210 Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel L1210 Ws 1\
subGroups view=WaveSignal cellType=L1210 sex=F treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipL1210FWaveSignalRep1\
type bigWig -17.782591 5.268431\

wgEncodeSydhHistMelH3k36me3bDm2p5dStdPk	MEL H3K36m3 DMSO	narrowPeak	MEL H3K36me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH	1	29	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K36me3 DMSO 2% Histone Mods by ChIP-seq Peaks from ENCODE/SYDH\
parent wgEncodeSydhHistViewPeaks off\
shortLabel MEL H3K36m3 DMSO\
subGroups view=Peaks factor=H3K36ME3b cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k36me3bDm2p5dStdPk\
type narrowPeak\

wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep2	Bcell (CD43-) S 2	bigWig 1.000000 76500.000000	B-cell (CD43-) DNaseI HS Signal Rep 2 from ENCODE/UW	2	30	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel B-cell (CD43-) DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Bcell (CD43-) S 2\
subGroups view=Signal age=ADULT8WKS cellType=BCELLCD43N sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseBcellcd43nC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 76500.000000\

wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xPkRep1	C2 Myogenin 24h 1	narrowPeak	C2C12 Myogenin Myocyte 24h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	30	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Myogenin Myocyte 24h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 Myogenin 24h 1\
subGroups view=Peaks factor=SC12732 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xPkRep1\
type narrowPeak\

wgEncodeLicrHistoneCbellumH3k4me3MAdult8wksC57bl6StdSig	Cbellum H3K4m3	bigWig 0.140000 49.660000	Cerebellum 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	30	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Cbellum H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCbellumH3k4me3MAdult8wksC57bl6StdSig\
type bigWig 0.140000 49.660000\
viewLimits 0.2:10\

wgEncodeSydhTfbsCh12NelfeIggrabSig	CH12 NELFe	bigWig 1.000000 127356.000000	CH12 NELFe TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	30	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 NELFe TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 NELFe\
subGroups view=Signal factor=NELFE cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12NelfeIggrabSig\
type bigWig 1.000000 127356.000000\

wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep2	CNS E11.5 + 2	bigWig 1.000000 646546.000000	CNS E11.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	30	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E11.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel CNS E11.5 + 2\
subGroups view=PlusRawSignal age=E11HALF cellType=CNS rep=rep2\
track wgEncodeCshlLongRnaSeqCnsE11halfPlusRawRep2\
type bigWig 1.000000 646546.000000\

wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep2	Crbellum 8w A 2	bam	Cerebellum Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW	0	30	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Crbellum 8w A 2\
subGroups view=Alignments age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodePsuHistoneG1eH3k27me3ME0S129InputSig	G1E H3K27m3	bigWig 1.000000 480.000000	G1E H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	30	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E H3K27m3\
subGroups view=Signal age=E0 factor=H3K27ME3 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k27me3ME0S129InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:100\

wgEncodePsuRnaSeqG1eME0S129R2x99dPlusRawRep2	G1E P 2	bigWig 1.000000 1180106.000000	G1E 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	30	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E P 2\
subGroups view=PlusRawSignal age=E0 cellType=G1E readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqG1eME0S129R2x99dPlusRawRep2\
type bigWig 1.000000 1180106.000000\

wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputPk	G1E-ER TAL1 24hr	broadPeak	G1E-ER4 TAL1 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU	3	30	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 TAL1 Estradiol 24 hr TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks\
shortLabel G1E-ER TAL1 24hr\
subGroups view=Peaks age=E0 factor=TAL1 cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputPk\
type broadPeak\

wgEncodeLicrTfbsHeartInputMAdult8wksC57bl6StdSig	Heart 8w Input	bigWig 0.140000 73.459999	Heart Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	30	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Heart 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsHeartInputMAdult8wksC57bl6StdSig\
type bigWig 0.140000 73.459999\

wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep2	Heart 8wk Sg 2	bigWig 4.000000 65503.000000	Heart Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	30	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel Heart 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=HEART localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqHeartCellPapMAdult8wksC57bl6SigRep2\
type bigWig 4.000000 65503.000000\

wgEncodeUwDgfKidneyC57bl6MAdult8wksPkRep1	Kidney 8w P	narrowPeak	Kidney 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	30	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel Kidney 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=KIDNEY strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfKidneyC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeFsuRepliChipL1210FWaveSignalRep2	L1210 Ws 2	bigWig -18.702608 6.627410	L1210 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	30	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel L1210 Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel L1210 Ws 2\
subGroups view=WaveSignal cellType=L1210 sex=F treatment=NONE rep=rep2\
track wgEncodeFsuRepliChipL1210FWaveSignalRep2\
type bigWig -18.702608 6.627410\

wgEncodeSydhHistMelH3k36me3bDm2p5dStdSig	MEL H3K36m3 DMSO	bigWig 1.000000 45856.000000	MEL H3K36me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	30	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K36me3 DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel MEL H3K36m3 DMSO\
subGroups view=Signal factor=H3K36ME3b cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelH3k36me3bDm2p5dStdSig\
type bigWig 1.000000 45856.000000\

wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xSigRep1	C2 Myogenin 24h 1	bigWig 0.087100 417.784607	C2C12 Myogenin Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	31	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Myogenin Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Myogenin 24h 1\
subGroups view=Signal factor=SC12732 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p24hPcr2xSigRep1\
type bigWig 0.087100 417.784607\

wgEncodeLicrHistoneCbellumH3k27acMAdult8wksC57bl6StdPk	Cbellum H3K27a	broadPeak	Cerebellum 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	31	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Cbellum H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCbellumH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseCerebellumC57bl6MAdult8wksHotspotsRep1	Cerebellum H 1	broadPeak	Cerebellum DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	31	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots\
shortLabel Cerebellum H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=CBELLUM sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseCerebellumC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeSydhTfbsCh12Nrf2IggrabPk	CH12 Nrf2 P	narrowPeak	CH12 Nrf2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	31	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 Nrf2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 Nrf2 P\
subGroups view=Peaks factor=NRF2 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Nrf2IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE11halfContigs	CNS E11.5 C	bed 6 +	CNS E11.5 Long RNA-seq Contigs from ENCODE/CSHL	3	31	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E11.5 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel CNS E11.5 C\
subGroups view=Contigs age=E11HALF cellType=CNS rep=repP\
track wgEncodeCshlLongRnaSeqCnsE11halfContigs\
type bed 6 +\

wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep1	Crbellum 8w MR 1	bigWig 1.000000 27993.000000	Cerebellum Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	31	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Crbellum 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 27993.000000\

wgEncodePsuHistoneG1eH3k36me3ME0S129InputPk	G1E H3K36m3	broadPeak	G1E H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	31	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E H3K36m3\
subGroups view=Peaks age=E0 factor=H3K36ME3 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k36me3ME0S129InputPk\
type broadPeak\

wgEncodePsuRnaSeqG1eME0S129R2x99dMinusRawRep2	G1E M 2	bigWig -1930728.000000 -1.000000	G1E 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	31	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E M 2\
subGroups view=MinusRawSignal age=E0 cellType=G1E readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqG1eME0S129R2x99dMinusRawRep2\
type bigWig -1930728.000000 -1.000000\

wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputSig	G1E-ER TAL1 24hr	bigWig 1.000000 266.000000	G1E-ER4 TAL1 Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU	2	31	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 TAL1 Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal\
shortLabel G1E-ER TAL1 24hr\
subGroups view=Signal age=E0 factor=TAL1 cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2Tal1ME0S129InputSig\
type bigWig 1.000000 266.000000\
viewLimits 1:100\

wgEncodeLicrTfbsHeartInputUE14halfC57bl6StdSig	Heart 14.5 Input	bigWig 0.140000 48.220001	Heart Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR	2	31	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Heart 14.5 Input\
subGroups view=Signal age=E14HALF factor=INPUT cellType=HEART control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsHeartInputUE14halfC57bl6StdSig\
type bigWig 0.140000 48.220001\

wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep1	Heart E14.5 Sg 1	bigWig 0.000000 65261.000000	Heart Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR	2	31	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Heart E14.5 Sg 1\
subGroups view=Signal age=E14HALF cellType=HEART localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep1\
type bigWig 0.000000 65261.000000\

wgEncodeUwDgfKidneyC57bl6MAdult8wksRawRep1	Kidney 8w R	bigWig 1.000000 267973.000000	Kidney 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	31	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel Kidney 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=KIDNEY strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfKidneyC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 267973.000000\

wgEncodeFsuRepliChipMefMWaveSignalRep1	MEF Ws 1	bigWig -5.096592 2.062456	MEF Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	31	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip off\
shortLabel MEF Ws 1\
subGroups view=WaveSignal cellType=MEF sex=M treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipMefMWaveSignalRep1\
type bigWig -5.096592 2.062456\

wgEncodeSydhHistMelInputIggrabSig	MEL Input rab	bigWig 1.000000 103648.000000	MEL Input IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	31	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Input IgG-rab Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel MEL Input rab\
subGroups view=Signal factor=zInputIGGRAB cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhHistMelInputIggrabSig\
type bigWig 1.000000 103648.000000\

wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xPkRep1	C2 Myogenin 60h 1	narrowPeak	C2C12 Myogenin Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	32	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Myogenin Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks\
shortLabel C2 Myogenin 60h 1\
subGroups view=Peaks factor=SC12732 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xPkRep1\
type narrowPeak\

wgEncodeLicrHistoneCbellumH3k27acMAdult8wksC57bl6StdSig	Cbellum H3K27a	bigWig 0.110000 27.700001	Cerebellum 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	32	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Cbellum H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCbellumH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.110000 27.700001\
viewLimits 0.2:5\

wgEncodeUwDnaseCerebellumC57bl6MAdult8wksPkRep1	Cerebellum P 1	narrowPeak	Cerebellum DNaseI HS Peaks Rep 1 from ENCODE/UW	3	32	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks\
shortLabel Cerebellum P 1\
subGroups view=Peaks age=ADULT8WKS cellType=CBELLUM sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseCerebellumC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeSydhTfbsCh12Nrf2IggrabSig	CH12 Nrf2 S	bigWig 1.000000 69455.000000	CH12 Nrf2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	32	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Nrf2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 Nrf2 S\
subGroups view=Signal factor=NRF2 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Nrf2IggrabSig\
type bigWig 1.000000 69455.000000\

wgEncodeCshlLongRnaSeqCnsE11halfJunctions	CNS E11.5 J	bed 6 +	CNS E11.5 Long RNA-seq Junctions from ENCODE/CSHL	0	32	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E11.5 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel CNS E11.5 J\
subGroups view=SJunctions age=E11HALF cellType=CNS rep=repP\
track wgEncodeCshlLongRnaSeqCnsE11halfJunctions\
type bed 6 +\

wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep2	Crbellum 8w MR 2	bigWig 1.000000 74939.000000	Cerebellum Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	32	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Crbellum 8w MR 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6MinusRawRep2\
type bigWig 1.000000 74939.000000\

wgEncodePsuRnaSeqG1eME0S129R2x99dAlnRep2	G1E A 2	bam	G1E 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU	0	32	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E A 2\
subGroups view=Alignments age=E0 cellType=G1E readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqG1eME0S129R2x99dAlnRep2\
type bam\

wgEncodePsuHistoneG1eH3k36me3ME0S129InputSig	G1E H3K36m3	bigWig 1.000000 480.000000	G1E H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	32	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E H3K36m3\
subGroups view=Signal age=E0 factor=H3K36ME3 cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eH3k36me3ME0S129InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:400\

wgEncodePsuTfbsG1eer4e2InputME0S129InputSig	G1E-ER Input 24hr	bigWig 1.000000 158.000000	G1E-ER4 Input Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU	2	32	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Input Estradiol 24 hr TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER Input 24hr\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1EER4 control=INPUT treatment=eDIFFD24H rep=repP sex=M strain=s129\
track wgEncodePsuTfbsG1eer4e2InputME0S129InputSig\
type bigWig 1.000000 158.000000\

wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdPk	Heart 8w p300	broadPeak	Heart Adult 8 weeks p300 TFBS ChIP-seq Peaks from ENCODE/LICR	3	32	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart Adult 8 weeks p300 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks\
shortLabel Heart 8w p300\
subGroups view=Peaks age=A1DULT8WKS factor=P300 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep2	Heart E14.5 Sg 2	bigWig 0.000000 65529.000000	Heart Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR	2	32	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Heart E14.5 Sg 2\
subGroups view=Signal age=E14HALF cellType=HEART localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqHeartCellPapUE14halfC57bl6SigRep2\
type bigWig 0.000000 65529.000000\

wgEncodeUwDgfKidneyC57bl6MAdult8wksSigRep1	Kidney 8w S	bigWig 1.000000 71303.000000	Kidney 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	32	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel Kidney 8w S\
subGroups view=Signal age=ADULT8WKS cellType=KIDNEY strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfKidneyC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 71303.000000\

wgEncodeSydhHistMelInputDm2p5dIggyaleSig	MEL Input DMSO Y	bigWig 1.000000 78459.000000	MEL Input DMSO 2% IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	32	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Input DMSO 2% IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel MEL Input DMSO Y\
subGroups view=Signal factor=zInputIGGYALE cellType=MEL control=IGGYale treatment=DM2P5D\
track wgEncodeSydhHistMelInputDm2p5dIggyaleSig\
type bigWig 1.000000 78459.000000\

wgEncodeFsuRepliChipMelMWaveSignalRep1	MEL Ws 1	bigWig -1.771599 1.324733	MEL Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU	0	32	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Repli-chip Wavelet-smoothed Signal Rep 1 from ENCODE/FSU\
parent wgEncodeFsuRepliChip\
shortLabel MEL Ws 1\
subGroups view=WaveSignal cellType=MEL sex=M treatment=NONE rep=rep1\
track wgEncodeFsuRepliChipMelMWaveSignalRep1\
type bigWig -1.771599 1.324733\

wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xSigRep1	C2 Myogenin 60h 1	bigWig 0.049800 296.461395	C2C12 Myogenin Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	33	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Myogenin Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal\
shortLabel C2 Myogenin 60h 1\
subGroups view=Signal factor=SC12732 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bE2p60hPcr2xSigRep1\
type bigWig 0.049800 296.461395\

wgEncodeLicrHistoneCbellumH3k27me3MAdult8wksC57bl6StdPk	Cbellum H3K27m3	broadPeak	Cerebellum 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	33	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Cbellum H3K27m3\
subGroups view=Peaks age=A1DLT8W factor=H3K27ME3 cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCbellumH3k27me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseCerebellumC57bl6MAdult8wksSigRep1	Cerebellum S 1	bigWig 1.000000 21846.000000	Cerebellum DNaseI HS Signal Rep 1 from ENCODE/UW	2	33	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal\
shortLabel Cerebellum S 1\
subGroups view=Signal age=ADULT8WKS cellType=CBELLUM sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseCerebellumC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 21846.000000\

wgEncodeSydhTfbsCh12P300sc584IggrabPk	CH12 p300 SC-584	narrowPeak	CH12 p300 (SC-584) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	33	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 p300 (SC-584) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks\
shortLabel CH12 p300 SC-584\
subGroups view=Peaks factor=P300SC584 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12P300sc584IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE14AlnRep1	CNS E14 Aln 1	bam	CNS E14 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	33	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E14 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel CNS E14 Aln 1\
subGroups view=Alignments age=E14 cellType=CNS rep=rep1\
track wgEncodeCshlLongRnaSeqCnsE14AlnRep1\
type bam\

wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep1	Crbellum 8w PR 1	bigWig 1.000000 15201.000000	Cerebellum Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	33	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Crbellum 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 15201.000000\

wgEncodePsuHistoneG1eInputME0S129InputSig	G1E Input	bigWig 1.000000 228.000000	G1E Input Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	33	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E Input Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E Input\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1E control=INPUT treatment=aNONE sex=M strain=s129\
track wgEncodePsuHistoneG1eInputME0S129InputSig\
type bigWig 1.000000 228.000000\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputPkRep1	G1E-ER GATA1 0hr	broadPeak	G1E-ER4 GATA1 Estradiol 0 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU	3	33	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 0 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E-ER GATA1 0hr\
subGroups view=Peaks age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputPkRep1\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hSigRep1	G1E-ER4 24hr S 1	bigWig 1.000000 167377.000000	G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Signal Rep 1 from ENCODE/PSU	2	33	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal off\
shortLabel G1E-ER4 24hr S 1\
subGroups view=Signal age=E0 cellType=G1EER4 readType=R1X36 sex=M strain=s129 treatment=fDIFFD24H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hSigRep1\
type bigWig 1.000000 167377.000000\

wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdSig	Heart 8w p300	bigWig 0.150000 53.220001	Heart Adult 8 weeks p300 TFBS ChIP-seq Signal from ENCODE/LICR	2	33	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks p300 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal\
shortLabel Heart 8w p300\
subGroups view=Signal age=A1DULT8WKS factor=P300 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsHeartP300MAdult8wksC57bl6StdSig\
type bigWig 0.150000 53.220001\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep1	Kidney 8wk Al 1	bam	Kidney Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	33	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Kidney 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=KIDNEY localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDgfLiverC57bl6MAdult8wksHotspotsRep1	Liver 8w H	broadPeak	Liver 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	33	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots\
shortLabel Liver 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=LIVER strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfLiverC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeSydhHistMelInputIggyaleSig	MEL Input Y	bigWig 1 80497	MEL Input IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	33	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Input IgG-Yale Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel MEL Input Y\
subGroups view=Signal factor=zInputIGGYALE cellType=MEL control=IGGYale treatment=zNONE\
track wgEncodeSydhHistMelInputIggyaleSig\
type bigWig 1 80497\

wgEncodeFsuRepliChipMelMWaveSignalRep2	MEL Ws 2	bigWig -2.123494 1.485932	MEL Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU	0	33	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Repli-chip Wavelet-smoothed Signal Rep 2 from ENCODE/FSU\
parent wgEncodeFsuRepliChip\
shortLabel MEL Ws 2\
subGroups view=WaveSignal cellType=MEL sex=M treatment=NONE rep=rep2\
track wgEncodeFsuRepliChipMelMWaveSignalRep2\
type bigWig -2.123494 1.485932\

wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xPkRep1	C2 Myogenin 1	narrowPeak	C2C12 Myogenin Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	34	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Myogenin Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 Myogenin 1\
subGroups view=Peaks factor=SC12732 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xPkRep1\
type narrowPeak\

wgEncodeLicrHistoneCbellumH3k27me3MAdult8wksC57bl6StdSig	Cbellum H3K27m3	bigWig 0.110000 40.980000	Cerebellum 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	34	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Cbellum H3K27m3\
subGroups view=Signal age=A1DLT8W factor=H3K27ME3 cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCbellumH3k27me3MAdult8wksC57bl6StdSig\
type bigWig 0.110000 40.980000\
viewLimits 0.2:2\

wgEncodeUwDnaseCbellumC57bl6MAdult8wksHotspotsRep2	Cerebellum H 2	broadPeak	Cerebellum DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	34	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Cerebellum H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=CBELLUM sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseCbellumC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeSydhTfbsCh12P300sc584IggrabSig	CH12 p300 SC-584	bigWig 1.000000 106426.000000	CH12 p300 (SC-584) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	34	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 p300 (SC-584) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig\
shortLabel CH12 p300 SC-584\
subGroups view=Signal factor=P300SC584 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12P300sc584IggrabSig\
type bigWig 1.000000 106426.000000\

wgEncodeCshlLongRnaSeqCnsE14MinusRawRep1	CNS E14 - 1	bigWig 1.000000 339669.000000	CNS E14 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	34	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E14 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel CNS E14 - 1\
subGroups view=MinusRawSignal age=E14 cellType=CNS rep=rep1\
track wgEncodeCshlLongRnaSeqCnsE14MinusRawRep1\
type bigWig 1.000000 339669.000000\

wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep2	Crbellum 8w PR 2	bigWig 1.000000 46134.000000	Cerebellum Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	34	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Crbellum 8w PR 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6PlusRawRep2\
type bigWig 1.000000 46134.000000\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputSigRep1	G1E-ER GATA1 0hr	bigWig 1.000000 298.000000	G1E-ER4 GATA1 Estradiol 0 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	34	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 0 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER GATA1 0hr\
subGroups view=Signal age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputSigRep1\
type bigWig 1.000000 298.000000\
viewLimits 1:100\

wgEncodePsuHistoneG1eer4e2H3k04me1ME0S129InputPk	G1E-ER H3K4m1 24	broadPeak	G1E-ER4 H3K4me1 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	34	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 H3K4me1 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E-ER H3K4m1 24\
subGroups view=Peaks age=E0 factor=H3K04ME1 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k04me1ME0S129InputPk\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hAlnRep1	G1E-ER4 24hr A 1	bam	G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Alignments Rep 1 from ENCODE/PSU	0	34	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 24hr A 1\
subGroups view=Alignments age=E0 cellType=G1EER4 readType=R1X36 sex=M strain=s129 treatment=fDIFFD24H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hAlnRep1\
type bam\

wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdPk	Heart 8w Pol2	broadPeak	Heart Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	34	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks\
shortLabel Heart 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep2	Kidney 8wk Al 2	bam	Kidney Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	34	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Kidney 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=KIDNEY localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDgfLiverC57bl6MAdult8wksPkRep1	Liver 8w P	narrowPeak	Liver 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	34	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks\
shortLabel Liver 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=LIVER strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfLiverC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeSydhHistMelInputDm2p5dStdSig	MEL Input DMSO	bigWig 1.000000 84376.000000	MEL Input DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH	2	34	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Input DMSO 2% Histone Mods by ChIP-seq Signal from ENCODE/SYDH\
parent wgEncodeSydhHistViewSig off\
shortLabel MEL Input DMSO\
subGroups view=Signal factor=zInputSTD cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhHistMelInputDm2p5dStdSig\
type bigWig 1.000000 84376.000000\

wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xSigRep1	C2 Myogenin 1	bigWig 0.171600 1243.264404	C2C12 Myogenin Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	35	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Myogenin Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Myogenin 1\
subGroups view=Signal factor=SC12732 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc12732FCntrl32bPcr2xSigRep1\
type bigWig 0.171600 1243.264404\

wgEncodeLicrHistoneCbellumInputMAdult8wksC57bl6StdSig	Cbellum Input	bigWig 0.140000 41.009998	Cerebellum 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	35	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Cbellum Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=CBELLUM control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCbellumInputMAdult8wksC57bl6StdSig\
type bigWig 0.140000 41.009998\
viewLimits 0.2:5\

wgEncodeUwDnaseCbellumC57bl6MAdult8wksPkRep2	Cerebellum P 2	narrowPeak	Cerebellum DNaseI HS Peaks Rep 2 from ENCODE/UW	3	35	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebellum DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Cerebellum P 2\
subGroups view=Peaks age=ADULT8WKS cellType=CBELLUM sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseCbellumC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeSydhTfbsCh12Pol2IggmusPk	CH12 Pol2	narrowPeak	CH12 Pol2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	35	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 Pol2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks\
shortLabel CH12 Pol2\
subGroups view=Peaks factor=POL2 cellType=CH12 control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsCh12Pol2IggmusPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE14PlusRawRep1	CNS E14 + 1	bigWig 1.000000 527651.000000	CNS E14 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	35	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E14 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel CNS E14 + 1\
subGroups view=PlusRawSignal age=E14 cellType=CNS rep=rep1\
track wgEncodeCshlLongRnaSeqCnsE14PlusRawRep1\
type bigWig 1.000000 527651.000000\

wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep1	Crbellum 8w S 1	bigWig 1.000000 27993.000000	Cerebellum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	35	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Crbellum 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 27993.000000\

wgEncodePsuHistoneG1eer4e2H3k04me1ME0S129InputSig	G1E-ER H3K4m1 24	bigWig 1.000000 480.000000	G1E-ER4 H3K4me1 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	35	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 H3K4me1 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E-ER H3K4m1 24\
subGroups view=Signal age=E0 factor=H3K04ME1 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k04me1ME0S129InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:300\

wgEncodePsuTfbsG1eer4InputME0S129InputSigRep1	G1E-ER Input 0hr	bigWig 1.000000 106.000000	G1E-ER4 Input Estradiol 0 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	35	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Input Estradiol 0 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER Input 0hr\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuTfbsG1eer4InputME0S129InputSigRep1\
type bigWig 1.000000 106.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hSigRep2	G1E-ER4 24hr S 2	bigWig 1.000000 162011.000000	G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Signal Rep 2 from ENCODE/PSU	2	35	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal off\
shortLabel G1E-ER4 24hr S 2\
subGroups view=Signal age=E0 cellType=G1EER4 readType=R1X36 sex=M strain=s129 treatment=fDIFFD24H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hSigRep2\
type bigWig 1.000000 162011.000000\

wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdSig	Heart 8w Pol2	bigWig 0.150000 50.889999	Heart Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	35	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal\
shortLabel Heart 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsHeartPol2MAdult8wksC57bl6StdSig\
type bigWig 0.150000 50.889999\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep1	Kidney 8wk Sg 1	bigWig 4.000000 65533.000000	Kidney Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	35	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Kidney 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=KIDNEY localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep1\
type bigWig 4.000000 65533.000000\

wgEncodeUwDgfLiverC57bl6MAdult8wksRawRep1	Liver 8w R	bigWig 1.000000 244216.000000	Liver 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	35	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal\
shortLabel Liver 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=LIVER strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfLiverC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 244216.000000\

wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xPkRep1	C2 Myogenin 7d 1	narrowPeak	C2C12 Myogenin Myocyte 7d TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	36	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 Myogenin Myocyte 7d TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 Myogenin 7d 1\
subGroups view=Peaks factor=SC12732 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P7D rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xPkRep1\
type narrowPeak\

wgEncodeUwDnaseCbellumC57bl6MAdult8wksSigRep2	Cerebellum S 2	bigWig 1.000000 19240.000000	Cerebellum DNaseI HS Signal Rep 2 from ENCODE/UW	2	36	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Cerebellum S 2\
subGroups view=Signal age=ADULT8WKS cellType=CBELLUM sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseCbellumC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 19240.000000\

wgEncodeLicrHistoneCh12H3k04me1FImmortalC57bl6StdPk	CH12 H3K4m1	broadPeak	CH12 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	36	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel CH12 H3K4m1\
subGroups view=Peaks age=IMMORTAL factor=H3K04ME1 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k04me1FImmortalC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsCh12Pol2IggmusSig	CH12 Pol2	bigWig 1 14925	CH12 Pol2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	36	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Pol2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig\
shortLabel CH12 Pol2\
subGroups view=Signal factor=POL2 cellType=CH12 control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsCh12Pol2IggmusSig\
type bigWig 1 14925\

wgEncodeCshlLongRnaSeqCnsE14AlnRep2	CNS E14 Aln 2	bam	CNS E14 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	36	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E14 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel CNS E14 Aln 2\
subGroups view=Alignments age=E14 cellType=CNS rep=rep2\
track wgEncodeCshlLongRnaSeqCnsE14AlnRep2\
type bam\

wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep2	Crbellum 8w S 2	bigWig 1.000000 74944.000000	Cerebellum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW	2	36	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebellum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Crbellum 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=CBELLUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqCbellumCellPolyaMAdult8wksC57bl6SigRep2\
type bigWig 1.000000 74944.000000\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hPkRep1	G1E-ER GATA1 3hr	broadPeak	G1E-ER4 GATA1 Estradiol 3 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU	3	36	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 3 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E-ER GATA1 3hr\
subGroups view=Peaks age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=bDIFFD3H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hPkRep1\
type broadPeak\

wgEncodePsuHistoneG1eer4e2H3k04me3ME0S129InputPk	G1E-ER H3K4m3 24	broadPeak	G1E-ER4 H3K4me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	36	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 H3K4me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E-ER H3K4m3 24\
subGroups view=Peaks age=E0 factor=H3K04ME3 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k04me3ME0S129InputPk\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hAlnRep2	G1E-ER4 24hr A 2	bam	G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Alignments Rep 2 from ENCODE/PSU	0	36	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 1x36 RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 24hr A 2\
subGroups view=Alignments age=E0 cellType=G1EER4 readType=R1X36 sex=M strain=s129 treatment=fDIFFD24H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R1x36Diffd24hAlnRep2\
type bam\

wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdPk	Kidney 8w CTCF	broadPeak	Kidney Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	36	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Kidney 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep2	Kidney 8wk Sg 2	bigWig 4.000000 65345.000000	Kidney Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	36	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Kidney 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=KIDNEY localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqKidneyCellPapMAdult8wksC57bl6SigRep2\
type bigWig 4.000000 65345.000000\

wgEncodeUwDgfLiverC57bl6MAdult8wksSigRep1	Liver 8w S	bigWig 1.000000 35245.000000	Liver 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	36	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal\
shortLabel Liver 8w S\
subGroups view=Signal age=ADULT8WKS cellType=LIVER strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfLiverC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 35245.000000\

wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xSigRep1	C2 Myogenin 7d 1	bigWig 0.055500 10654.280273	C2C12 Myogenin Myocyte 7d TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	37	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 Myogenin Myocyte 7d TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 Myogenin 7d 1\
subGroups view=Signal factor=SC12732 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P7D rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc12732FCntrl50bE2p7dPcr1xSigRep1\
type bigWig 0.055500 10654.280273\

wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep1	Cerebrum 8w A 1	bam	Cerebrum Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	37	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebrum Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Cerebrum 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=CEREBRUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep1	Cerebrum H 1	broadPeak	Cerebrum DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	37	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebrum DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots\
shortLabel Cerebrum H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=CEREBRUM sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneCh12H3k04me1FImmortalC57bl6StdSig	CH12 H3K4m1	bigWig 0.130000 18.420000	CH12 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	37	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel CH12 H3K4m1\
subGroups view=Signal age=IMMORTAL factor=H3K04ME1 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k04me1FImmortalC57bl6StdSig\
type bigWig 0.130000 18.420000\
viewLimits 0.2:3\

wgEncodeSydhTfbsCh12Pol2s2IggrabPk	CH12 Pol2S2	narrowPeak	CH12 Pol2(phoshoS2) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	37	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 Pol2(phoshoS2) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 Pol2S2\
subGroups view=Peaks factor=POL2S2 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Pol2s2IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE14MinusRawRep2	CNS E14 - 2	bigWig 1.000000 564636.000000	CNS E14 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	37	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E14 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel CNS E14 - 2\
subGroups view=MinusRawSignal age=E14 cellType=CNS rep=rep2\
track wgEncodeCshlLongRnaSeqCnsE14MinusRawRep2\
type bigWig 1.000000 564636.000000\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hSigRep1	G1E-ER GATA1 3hr	bigWig 1.000000 268.000000	G1E-ER4 GATA1 Estradiol 3 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	37	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 3 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER GATA1 3hr\
subGroups view=Signal age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=bDIFFD3H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd3hSigRep1\
type bigWig 1.000000 268.000000\
viewLimits 1:100\

wgEncodePsuHistoneG1eer4e2H3k04me3ME0S129InputSig	G1E-ER H3K4m3 24	bigWig 1.000000 480.000000	G1E-ER4 H3K4me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	37	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 H3K4me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E-ER H3K4m3 24\
subGroups view=Signal age=E0 factor=H3K04ME3 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k04me3ME0S129InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:250\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep1	G1E-ER4 0hr P 1	bigWig 1.000000 1255930.000000	G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	37	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 0hr P 1\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep1\
type bigWig 1.000000 1255930.000000\

wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdSig	Kidney 8w CTCF	bigWig 0.150000 51.889999	Kidney Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	37	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Kidney 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsKidneyCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.150000 51.889999\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep1	Limb E14.5 Al 1	bam	Limb Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR	0	37	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Limb E14.5 Al 1\
subGroups view=Alignments age=E14HALF cellType=LIMB localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep1\
type bam\

wgEncodeUwDgfLungC57bl6MAdult8wksHotspotsRep1	Lung 8w H	broadPeak	Lung 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	37	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel Lung 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=LUNG strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfLungC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xPkRep1	C2 MyoD 24h 1	narrowPeak	C2C12 MyoD Myocyte 24h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	38	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 MyoD Myocyte 24h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 MyoD 24h 1\
subGroups view=Peaks factor=SC32758 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xPkRep1\
type narrowPeak\

wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep2	Cerebrum 8w A 2	bam	Cerebrum Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW	0	38	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebrum Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Cerebrum 8w A 2\
subGroups view=Alignments age=ADULT8WKS cellType=CEREBRUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep1	Cerebrum P 1	narrowPeak	Cerebrum DNaseI HS Peaks Rep 1 from ENCODE/UW	3	38	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebrum DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks\
shortLabel Cerebrum P 1\
subGroups view=Peaks age=ADULT8WKS cellType=CEREBRUM sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeLicrHistoneCh12H3k04me2FImmortalC57bl6StdPk	CH12 H3K4m2	broadPeak	CH12 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	38	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K4me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel CH12 H3K4m2\
subGroups view=Peaks age=IMMORTAL factor=H3K04ME2 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k04me2FImmortalC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsCh12Pol2s2IggrabSig	CH12 Pol2S2	bigWig 1.000000 59971.000000	CH12 Pol2(phosphoS2) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	38	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Pol2(phosphoS2) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 Pol2S2\
subGroups view=Signal factor=POL2S2 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Pol2s2IggrabSig\
type bigWig 1.000000 59971.000000\

wgEncodeCshlLongRnaSeqCnsE14PlusRawRep2	CNS E14 + 2	bigWig 1.000000 935604.000000	CNS E14 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	38	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E14 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel CNS E14 + 2\
subGroups view=PlusRawSignal age=E14 cellType=CNS rep=rep2\
track wgEncodeCshlLongRnaSeqCnsE14PlusRawRep2\
type bigWig 1.000000 935604.000000\

wgEncodePsuHistoneG1eer4e2H3k09me3ME0S129InputPk	G1E-ER H3K9m3 24	broadPeak	G1E-ER4 H3K9me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	38	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 H3K9me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E-ER H3K9m3 24\
subGroups view=Peaks age=E0 factor=H3K09ME3 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k09me3ME0S129InputPk\
type broadPeak\

wgEncodePsuTfbsG1eer4InputME0S129InputDiffd3hSigRep1	G1E-ER Input 3hr	bigWig 1.000000 90.000000	G1E-ER4 Input Estradiol 3 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	38	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Input Estradiol 3 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER Input 3hr\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=bDIFFD3H rep=rep1\
track wgEncodePsuTfbsG1eer4InputME0S129InputDiffd3hSigRep1\
type bigWig 1.000000 90.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep1	G1E-ER4 0hr M 1	bigWig -1764097.000000 -1.000000	G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	38	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 0hr M 1\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep1\
type bigWig -1764097.000000 -1.000000\

wgEncodeLicrTfbsKidneyInputMAdult8wksC57bl6StdSig	Kidney 8w Input	bigWig 0.140000 51.650002	Kidney Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	38	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Kidney 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsKidneyInputMAdult8wksC57bl6StdSig\
type bigWig 0.140000 51.650002\

wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep2	Limb E14.5 Al 2	bam	Limb Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR	0	38	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Limb E14.5 Al 2\
subGroups view=Alignments age=E14HALF cellType=LIMB localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6AlnRep2\
type bam\

wgEncodeUwDgfLungC57bl6MAdult8wksPkRep1	Lung 8w P	narrowPeak	Lung 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	38	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel Lung 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=LUNG strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfLungC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xSigRep1	C2 MyoD 24h 1	bigWig 0.052100 827.875977	C2C12 MyoD Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	39	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 MyoD Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 MyoD 24h 1\
subGroups view=Signal factor=SC32758 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p24hPcr2xSigRep1\
type bigWig 0.052100 827.875977\

wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep1	Cerebrum 8w MR 1	bigWig 1.000000 363975.000000	Cerebrum Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	39	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebrum Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel Cerebrum 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=CEREBRUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 363975.000000\

wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep1	Cerebrum S 1	bigWig 1.000000 40784.000000	Cerebrum DNaseI HS Signal Rep 1 from ENCODE/UW	2	39	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebrum DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal\
shortLabel Cerebrum S 1\
subGroups view=Signal age=ADULT8WKS cellType=CEREBRUM sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 40784.000000\

wgEncodeLicrHistoneCh12H3k04me2FImmortalC57bl6StdSig	CH12 H3K4m2	bigWig 0.130000 33.910000	CH12 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	39	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K4me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel CH12 H3K4m2\
subGroups view=Signal age=IMMORTAL factor=H3K04ME2 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k04me2FImmortalC57bl6StdSig\
type bigWig 0.130000 33.910000\
viewLimits 0.2:3\

wgEncodeSydhTfbsCh12Rad21IggrabPk	CH12 Rad21	narrowPeak	CH12 Rad21 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	39	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 Rad21 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 Rad21\
subGroups view=Peaks factor=RAD21 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Rad21IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE14Contigs	CNS E14 C	bed 6 +	CNS E14 Long RNA-seq Contigs from ENCODE/CSHL	3	39	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E14 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel CNS E14 C\
subGroups view=Contigs age=E14 cellType=CNS rep=repP\
track wgEncodeCshlLongRnaSeqCnsE14Contigs\
type bed 6 +\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hPkRep1	G1E-ER GATA1 7hr	broadPeak	G1E-ER4 GATA1 Estradiol 7 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU	3	39	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 7 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E-ER GATA1 7hr\
subGroups view=Peaks age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=cDIFFD7H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hPkRep1\
type broadPeak\

wgEncodePsuHistoneG1eer4e2H3k09me3ME0S129InputSig	G1E-ER H3K9m3 24	bigWig 1.000000 480.000000	G1E-ER4 H3K9me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	39	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 H3K9me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E-ER H3K9m3 24\
subGroups view=Signal age=E0 factor=H3K09ME3 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k09me3ME0S129InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:100\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dAlnRep1	G1E-ER4 0hr A 1	bam	G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU	0	39	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 0hr A 1\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dAlnRep1\
type bam\

wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdPk	Kidney 8w Pol2	broadPeak	Kidney Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	39	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Kidney 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep1	Limb E14.5 Sg 1	bigWig 0.000000 65535.000000	Limb Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR	2	39	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Limb E14.5 Sg 1\
subGroups view=Signal age=E14HALF cellType=LIMB localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep1\
type bigWig 0.000000 65535.000000\

wgEncodeUwDgfLungC57bl6MAdult8wksRawRep1	Lung 8w R	bigWig 1.000000 377717.000000	Lung 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	39	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel Lung 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=LUNG strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfLungC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 377717.000000\

wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xPkRep1	C2 MyoD 60h 1	narrowPeak	C2C12 MyoD Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	40	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 MyoD Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 MyoD 60h 1\
subGroups view=Peaks factor=SC32758 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xPkRep1\
type narrowPeak\

wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep2	Cerebrum 8w MR 2	bigWig 1.000000 102922.000000	Cerebrum Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	40	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebrum Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel Cerebrum 8w MR 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=CEREBRUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6MinusRawRep2\
type bigWig 1.000000 102922.000000\

wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep2	Cerebrum H 2	broadPeak	Cerebrum DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	40	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebrum DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Cerebrum H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=CEREBRUM sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseCerebrumC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneCh12H3k04me3FImmortalC57bl6StdPk	CH12 H3K4m3	broadPeak	CH12 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	40	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel CH12 H3K4m3\
subGroups view=Peaks age=IMMORTAL factor=H3K04ME3 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k04me3FImmortalC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsCh12Rad21IggrabSig	CH12 Rad21	bigWig 1.000000 78996.000000	CH12 Rad21 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	40	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Rad21 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 Rad21\
subGroups view=Signal factor=RAD21 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Rad21IggrabSig\
type bigWig 1.000000 78996.000000\

wgEncodeCshlLongRnaSeqCnsE14Junctions	CNS E14 J	bed 6 +	CNS E14 Long RNA-seq Junctions from ENCODE/CSHL	0	40	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E14 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel CNS E14 J\
subGroups view=SJunctions age=E14 cellType=CNS rep=repP\
track wgEncodeCshlLongRnaSeqCnsE14Junctions\
type bed 6 +\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hSigRep1	G1E-ER GATA1 7hr	bigWig 1.000000 276.000000	G1E-ER4 GATA1 Estradiol 7 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	40	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 7 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER GATA1 7hr\
subGroups view=Signal age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=cDIFFD7H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd7hSigRep1\
type bigWig 1.000000 276.000000\
viewLimits 1:100\

wgEncodePsuHistoneG1eer4e2H3k27me3ME0S129InputPk	G1E-ER H3K27m3 24	broadPeak	G1E-ER4 H3K27me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	40	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 H3K27me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E-ER H3K27m3 24\
subGroups view=Peaks age=E0 factor=H3K27ME3 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k27me3ME0S129InputPk\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep2	G1E-ER4 0hr P 2	bigWig 1.000000 766123.000000	G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq  Plus Raw Signal Rep 2 from ENCODE/PSU	2	40	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq  Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 0hr P 2\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dPlusRawRep2\
type bigWig 1.000000 766123.000000\

wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdSig	Kidney 8w Pol2	bigWig 0.140000 40.459999	Kidney Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	40	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Kidney 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsKidneyPol2MAdult8wksC57bl6StdSig\
type bigWig 0.140000 40.459999\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep2	Limb E14.5 Sg 2	bigWig 0.000000 65513.000000	Limb Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR	2	40	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Limb E14.5 Sg 2\
subGroups view=Signal age=E14HALF cellType=LIMB localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqLimbCellPapUE14halfC57bl6SigRep2\
type bigWig 0.000000 65513.000000\

wgEncodeUwDgfLungC57bl6MAdult8wksSigRep1	Lung 8w S	bigWig 1.000000 44724.000000	Lung 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	40	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel Lung 8w S\
subGroups view=Signal age=ADULT8WKS cellType=LUNG strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfLungC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 44724.000000\

wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xSigRep1	C2 MyoD 60h 1	bigWig 0.033900 335.904602	C2C12 MyoD Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	41	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 MyoD Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 MyoD 60h 1\
subGroups view=Signal factor=SC32758 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bE2p60hPcr2xSigRep1\
type bigWig 0.033900 335.904602\

wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep1	Cerebrum 8w PR 1	bigWig 1.000000 267152.000000	Cerebrum Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	41	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebrum Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel Cerebrum 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=CEREBRUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 267152.000000\

wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep2	Cerebrum P 2	narrowPeak	Cerebrum DNaseI HS Peaks Rep 2 from ENCODE/UW	3	41	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cerebrum DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Cerebrum P 2\
subGroups view=Peaks age=ADULT8WKS cellType=CEREBRUM sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseCerebrumC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeLicrHistoneCh12H3k04me3FImmortalC57bl6StdSig	CH12 H3K4m3	bigWig 0.120000 42.500000	CH12 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	41	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel CH12 H3K4m3\
subGroups view=Signal age=IMMORTAL factor=H3K04ME3 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k04me3FImmortalC57bl6StdSig\
type bigWig 0.120000 42.500000\
viewLimits 0.2:10\

wgEncodeSydhTfbsCh12Sin3anb6001263IggrabPk	CH12 SIN3A_N	narrowPeak	CH12 SIN3A (NB600-1263) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	41	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 SIN3A (NB600-1263) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 SIN3A_N\
subGroups view=Peaks factor=SIN3ANB6001263 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Sin3anb6001263IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE18AlnRep1	CNS E18 Aln 1	bam	CNS E18 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	41	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E18 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel CNS E18 Aln 1\
subGroups view=Alignments age=E18 cellType=CNS rep=rep1\
track wgEncodeCshlLongRnaSeqCnsE18AlnRep1\
type bam\

wgEncodePsuHistoneG1eer4e2H3k27me3ME0S129InputSig	G1E-ER H3K27m3 24	bigWig 1.000000 480.000000	G1E-ER4 H3K27me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	41	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 H3K27me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E-ER H3K27m3 24\
subGroups view=Signal age=E0 factor=H3K27ME3 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k27me3ME0S129InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:150\

wgEncodePsuTfbsG1eer4InputME0S129InputDiffd7hSigRep1	G1E-ER Input 7hr	bigWig 1.000000 112.000000	G1E-ER4 Input Estradiol 7 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	41	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Input Estradiol 7 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER Input 7hr\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=cDIFFD7H rep=rep1\
track wgEncodePsuTfbsG1eer4InputME0S129InputDiffd7hSigRep1\
type bigWig 1.000000 112.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep2	G1E-ER4 0hr M 2	bigWig -1193225.000000 -1.000000	G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	41	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 0hr M 2\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dMinusRawRep2\
type bigWig -1193225.000000 -1.000000\

wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdPk	Limb 14.5 CTCF	broadPeak	Limb Embryonic day 14.5 CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	41	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb Embryonic day 14.5 CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Limb 14.5 CTCF\
subGroups view=Peaks age=E14HALF factor=CTCF cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep1	Liver 8wk Al 1	bam	Liver Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	41	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Liver 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDgfMelUknImmortalHotspotsRep1	MEL Immt H	broadPeak	MEL Immortal DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	41	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Immortal DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots\
shortLabel MEL Immt H\
subGroups view=Hotspots age=IMMORTAL cellType=MEL strain=UKN treatment=NONE rep=rep1\
track wgEncodeUwDgfMelUknImmortalHotspotsRep1\
type broadPeak\

wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xPkRep1	C2 MyoD 24h 1	narrowPeak	C2C12 MyoD Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	42	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 MyoD Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks\
shortLabel C2 MyoD 24h 1\
subGroups view=Peaks factor=SC32758 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xPkRep1\
type narrowPeak\

wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep2	Cerebrum 8w PR 2	bigWig 1.000000 49715.000000	Cerebrum Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	42	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebrum Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel Cerebrum 8w PR 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=CEREBRUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6PlusRawRep2\
type bigWig 1.000000 49715.000000\

wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep2	Cerebrum S 2	bigWig 1.000000 19185.000000	Cerebrum DNaseI HS Signal Rep 2 from ENCODE/UW	2	42	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebrum DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Cerebrum S 2\
subGroups view=Signal age=ADULT8WKS cellType=CEREBRUM sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseCerebrumC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 19185.000000\

wgEncodeLicrHistoneCh12H3k09acFImmortalC57bl6StdPk	CH12 H3K9a	broadPeak	CH12 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	42	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel CH12 H3K9a\
subGroups view=Peaks age=IMMORTAL factor=H3K09AC cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k09acFImmortalC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsCh12Sin3anb6001263IggrabSig	CH12 SIN3A_N	bigWig 1.000000 159622.000000	CH12 SIN3A (NB600-1263) IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	42	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 SIN3A (NB600-1263) IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 SIN3A_N\
subGroups view=Signal factor=SIN3ANB6001263 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Sin3anb6001263IggrabSig\
type bigWig 1.000000 159622.000000\

wgEncodeCshlLongRnaSeqCnsE18MinusRawRep1	CNS E18 - 1	bigWig 1.000000 474002.000000	CNS E18 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	42	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E18 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel CNS E18 - 1\
subGroups view=MinusRawSignal age=E18 cellType=CNS rep=rep1\
track wgEncodeCshlLongRnaSeqCnsE18MinusRawRep1\
type bigWig 1.000000 474002.000000\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hPkRep1	G1E-ER GATA1 14hr	broadPeak	G1E-ER4 GATA1 Estradiol 14 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU	3	42	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 14 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E-ER GATA1 14hr\
subGroups view=Peaks age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=dDIFFD14H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hPkRep1\
type broadPeak\

wgEncodePsuHistoneG1eer4e2H3k36me3BE0S129InputPk	G1E-ER H3K36m3 24	broadPeak	G1E-ER4 H3K36me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	42	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 H3K36me3 Estradiol 24 hr Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks off\
shortLabel G1E-ER H3K36m3 24\
subGroups view=Peaks age=E0 factor=H3K36ME3 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k36me3BE0S129InputPk\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dAlnRep2	G1E-ER4 0hr A 2	bam	G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU	0	42	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 0 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 0hr A 2\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dAlnRep2\
type bam\

wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdSig	Limb 14.5 CTCF	bigWig 0.150000 78.269997	Limb Embryonic day 14.5 CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	42	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb Embryonic day 14.5 CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Limb 14.5 CTCF\
subGroups view=Signal age=E14HALF factor=CTCF cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsLimbCtcfUE14halfC57bl6StdSig\
type bigWig 0.150000 78.269997\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep2	Liver 8wk Al 2	bam	Liver Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	42	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Liver 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDgfMelUknImmortalPkRep1	MEL Immt P	narrowPeak	MEL Immortal DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	42	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Immortal DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks\
shortLabel MEL Immt P\
subGroups view=Peaks age=IMMORTAL cellType=MEL strain=UKN treatment=NONE rep=rep1\
track wgEncodeUwDgfMelUknImmortalPkRep1\
type narrowPeak\

wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xSigRep1	C2 MyoD 1	bigWig 0.049800 999.933289	C2C12 MyoD Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	43	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 MyoD Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal\
shortLabel C2 MyoD 1\
subGroups view=Signal factor=SC32758 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc32758FCntrl32bPcr2xSigRep1\
type bigWig 0.049800 999.933289\

wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep1	Cerebrum 8w S 1	bigWig 1.000000 363975.000000	Cerebrum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	43	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebrum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel Cerebrum 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=CEREBRUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 363975.000000\

wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep1	CH12 H 1	broadPeak	CH12 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	43	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel CH12 H 1\
subGroups view=Hotspots age=IMMORTAL cellType=CH12 sex=F strain=b2A4B treatment=zNONE rep=rep1\
track wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneCh12H3k09acFImmortalC57bl6StdSig	CH12 H3K9a	bigWig 0.110000 26.100000	CH12 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	43	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel CH12 H3K9a\
subGroups view=Signal age=IMMORTAL factor=H3K09AC cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k09acFImmortalC57bl6StdSig\
type bigWig 0.110000 26.100000\
viewLimits 0.2:5\

wgEncodeSydhTfbsCh12Smc3ab9263IggrabPk	CH12 SMC3	narrowPeak	CH12 SMC3 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	43	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 SMC3 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 SMC3\
subGroups view=Peaks factor=SMC3ab9263 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Smc3ab9263IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE18PlusRawRep1	CNS E18 + 1	bigWig 1.000000 311688.000000	CNS E18 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	43	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E18 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel CNS E18 + 1\
subGroups view=PlusRawSignal age=E18 cellType=CNS rep=rep1\
track wgEncodeCshlLongRnaSeqCnsE18PlusRawRep1\
type bigWig 1.000000 311688.000000\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hSigRep1	G1E-ER GATA1 14hr	bigWig 1.000000 214.000000	G1E-ER4 GATA1 Estradiol 14 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	43	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 14 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER GATA1 14hr\
subGroups view=Signal age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=dDIFFD14H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd14hSigRep1\
type bigWig 1.000000 214.000000\
viewLimits 1:100\

wgEncodePsuHistoneG1eer4e2H3k36me3BE0S129InputSig	G1E-ER H3K36m3 24	bigWig 1.000000 479.000000	G1E-ER4 H3K36me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	43	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 H3K36me3 Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E-ER H3K36m3 24\
subGroups view=Signal age=E0 factor=H3K36ME3 cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2H3k36me3BE0S129InputSig\
type bigWig 1.000000 479.000000\
viewLimits 2:400\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hPlusRawRep1	G1E-ER4 3hr P 1	bigWig 1.000000 1780000.000000	G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	43	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 3hr P 1\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=cDIFFD3H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hPlusRawRep1\
type bigWig 1.000000 1780000.000000\

wgEncodeLicrTfbsLimbInputUE14halfC57bl6StdSig	Limb 14.5 Input	bigWig 0.150000 46.419998	Limb Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR	2	43	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Limb 14.5 Input\
subGroups view=Signal age=E14HALF factor=INPUT cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsLimbInputUE14halfC57bl6StdSig\
type bigWig 0.150000 46.419998\

wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep1	Liver E14.5 Al 1	bam	Liver Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR	0	43	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Liver E14.5 Al 1\
subGroups view=Alignments age=E14HALF cellType=LIVER localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep1\
type bam\

wgEncodeUwDgfMelUknImmortalRawRep1	MEL Immt R	bigWig 1.000000 974470.000000	MEL Immortal DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	43	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal\
shortLabel MEL Immt R\
subGroups view=RawSignal age=IMMORTAL cellType=MEL strain=UKN treatment=NONE rep=rep1\
track wgEncodeUwDgfMelUknImmortalRawRep1\
type bigWig 1.000000 974470.000000\

wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xPkRep1	C2 MyoD 7d 1	narrowPeak	C2C12 MyoD Myocyte 7d TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	44	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 MyoD Myocyte 7d TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 MyoD 7d 1\
subGroups view=Peaks factor=SC32758 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P7D rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xPkRep1\
type narrowPeak\

wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep2	Cerebrum 8w S 2	bigWig 1.000000 103007.000000	Cerebrum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW	2	44	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cerebrum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel Cerebrum 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=CEREBRUM localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqCerebrumCellPolyaMAdult8wksC57bl6SigRep2\
type bigWig 1.000000 103007.000000\

wgEncodeLicrHistoneCh12H3k27acFImmortalC57bl6StdPk	CH12 H3K27a	broadPeak	CH12 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	44	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel CH12 H3K27a\
subGroups view=Peaks age=IMMORTAL factor=H3K27AC cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k27acFImmortalC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseCh122a4bFImmortalPkRep1	CH12 P 1	narrowPeak	CH12 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	44	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel CH12 P 1\
subGroups view=Peaks age=IMMORTAL cellType=CH12 sex=F strain=b2A4B treatment=zNONE rep=rep1\
track wgEncodeUwDnaseCh122a4bFImmortalPkRep1\
type narrowPeak\

wgEncodeSydhTfbsCh12Smc3ab9263IggrabSig	CH12 SMC3	bigWig 1.000000 105075.000000	CH12 SMC3 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	44	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 SMC3 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 SMC3\
subGroups view=Signal factor=SMC3ab9263 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Smc3ab9263IggrabSig\
type bigWig 1.000000 105075.000000\

wgEncodeCshlLongRnaSeqCnsE18AlnRep2	CNS E18 Aln 2	bam	CNS E18 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	44	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E18 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel CNS E18 Aln 2\
subGroups view=Alignments age=E18 cellType=CNS rep=rep2\
track wgEncodeCshlLongRnaSeqCnsE18AlnRep2\
type bam\

wgEncodePsuHistoneG1eer4e2InputME0S129InputSig	G1E-ER Input	bigWig 1.000000 158.000000	G1E-ER4 Input Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	44	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Input Estradiol 24 hr Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel G1E-ER Input\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1EER4 control=INPUT treatment=DIFFD24H sex=M strain=s129\
track wgEncodePsuHistoneG1eer4e2InputME0S129InputSig\
type bigWig 1.000000 158.000000\

wgEncodePsuTfbsG1eer4InputME0S129InputDiffd14hSigRep1	G1E-ER Input 14hr	bigWig 1.000000 114.000000	G1E-ER4 Input Estradiol 14 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	44	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Input Estradiol 14 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER Input 14hr\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=dDIFFD14H rep=rep1\
track wgEncodePsuTfbsG1eer4InputME0S129InputDiffd14hSigRep1\
type bigWig 1.000000 114.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hMinusRawRep1	G1E-ER4 3hr M 1	bigWig -2498335.000000 -1.000000	G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	44	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 3hr M 1\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=cDIFFD3H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hMinusRawRep1\
type bigWig -2498335.000000 -1.000000\

wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdPk	Limb 14.5 Pol2	broadPeak	Limb Embryonic day 14.5 Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	44	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb Embryonic day 14.5 Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Limb 14.5 Pol2\
subGroups view=Peaks age=E14HALF factor=POL2 cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep2	Liver E14.5 Al 2	bam	Liver Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR	0	44	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Liver E14.5 Al 2\
subGroups view=Alignments age=E14HALF cellType=LIVER localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6AlnRep2\
type bam\

wgEncodeUwDgfMelUknImmortalSigRep1	MEL Immt S	bigWig 1.000000 300871.000000	MEL Immortal DNaseI DGF Signal Rep 1 from ENCODE/UW	2	44	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal\
shortLabel MEL Immt S\
subGroups view=Signal age=IMMORTAL cellType=MEL strain=UKN treatment=NONE rep=rep1\
track wgEncodeUwDgfMelUknImmortalSigRep1\
type bigWig 1.000000 300871.000000\

wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xSigRep1	C2 MyoD 7d 1	bigWig 0.034500 10969.869141	C2C12 MyoD Myocyte 7d TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	45	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 MyoD Myocyte 7d TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 MyoD 7d 1\
subGroups view=Signal factor=SC32758 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P7D rep=rep1\
track wgEncodeCaltechTfbsC2c12Sc32758FCntrl50bE2p7dPcr1xSigRep1\
type bigWig 0.034500 10969.869141\

wgEncodeLicrHistoneCh12H3k27acFImmortalC57bl6StdSig	CH12 H3K27a	bigWig 0.140000 46.000000	CH12 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	45	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel CH12 H3K27a\
subGroups view=Signal age=IMMORTAL factor=H3K27AC cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k27acFImmortalC57bl6StdSig\
type bigWig 0.140000 46.000000\
viewLimits 0.2:5\

wgEncodeUwDnaseCh122a4bFImmortalSigRep1	CH12 S 1	bigWig 1.000000 162118.000000	CH12 DNaseI HS Signal Rep 1 from ENCODE/UW	2	45	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel CH12 S 1\
subGroups view=Signal age=IMMORTAL cellType=CH12 sex=F strain=b2A4B treatment=zNONE rep=rep1\
track wgEncodeUwDnaseCh122a4bFImmortalSigRep1\
type bigWig 1.000000 162118.000000\

wgEncodeSydhTfbsCh12TbpIggmusPk	CH12 TBP	narrowPeak	CH12 TBP TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	45	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 TBP TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 TBP\
subGroups view=Peaks factor=TBP cellType=CH12 control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsCh12TbpIggmusPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE18MinusRawRep2	CNS E18  - 2	bigWig 1.000000 700305.000000	CNS E18 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	45	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E18 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel CNS E18  - 2\
subGroups view=MinusRawSignal age=E18 cellType=CNS rep=rep2\
track wgEncodeCshlLongRnaSeqCnsE18MinusRawRep2\
type bigWig 1.000000 700305.000000\

wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6AlnRep1	FatPad 8w A 1	bam	FatPad Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	45	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel FatPad Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel FatPad 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=FAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hPkRep1	G1E-ER GATA1 24hr	broadPeak	G1E-ER4 GATA1 Estradiol 24 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU	3	45	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 24 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E-ER GATA1 24hr\
subGroups view=Peaks age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=eDIFFD24H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hPkRep1\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hAlnRep1	G1E-ER4 3hr A 1	bam	G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU	0	45	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 3hr A 1\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=cDIFFD3H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hAlnRep1\
type bam\

wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdSig	Limb 14.5 Pol2	bigWig 0.160000 84.010002	Limb Embryonic day 14.5 Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	45	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb Embryonic day 14.5 Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Limb 14.5 Pol2\
subGroups view=Signal age=E14HALF factor=POL2 cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsLimbPol2UE14halfC57bl6StdSig\
type bigWig 0.160000 84.010002\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep1	Liver 8wk Sg 1	bigWig 3.000000 65508.000000	Liver Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	45	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel Liver 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep1\
type bigWig 3.000000 65508.000000\

wgEncodePsuHistoneMegakaryoH3k04me1BE14halfCd1InputPk	Megakary H3K4m1	broadPeak	Megakaryocyte H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	45	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryocyte H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Megakary H3K4m1\
subGroups view=Peaks age=E14HALF factor=H3K04ME1 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k04me1BE14halfCd1InputPk\
type broadPeak\

wgEncodeUwDgfNih3t3NihsMImmortalHotspotsRep1	NIH-3T3 Immt H	broadPeak	NIH-3T3 Immortal NIH/Swiss DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	45	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel NIH-3T3 Immortal NIH/Swiss DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel NIH-3T3 Immt H\
subGroups view=Hotspots age=IMMORTAL cellType=NIH3T3 strain=NIHS treatment=NONE rep=rep1\
track wgEncodeUwDgfNih3t3NihsMImmortalHotspotsRep1\
type broadPeak\

wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xPkRep1	C2 SRF 24h 1	narrowPeak	C2C12 SRF Myocyte 24h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	46	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 SRF Myocyte 24h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 SRF 24h 1\
subGroups view=Peaks factor=SRF cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xPkRep1\
type narrowPeak\

wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep2	CH12 H 2	broadPeak	CH12 DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	46	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel CH12 H 2\
subGroups view=Hotspots age=IMMORTAL cellType=CH12 sex=F strain=b2A4B treatment=zNONE rep=rep2\
track wgEncodeUwDnaseCh122a4bFImmortalHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneCh12H3k36me3FImmortalC57bl6StdPk	CH12 H3K36m3	broadPeak	CH12 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	46	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel CH12 H3K36m3\
subGroups view=Peaks age=IMMORTAL factor=H3K36ME3 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k36me3FImmortalC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsCh12TbpIggmusSig	CH12 TBP	bigWig 1 52209	CH12 TBP TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	46	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 TBP TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 TBP\
subGroups view=Signal factor=TBP cellType=CH12 control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsCh12TbpIggmusSig\
type bigWig 1 52209\

wgEncodeCshlLongRnaSeqCnsE18PlusRawRep2	CNS E18 + 2	bigWig 1.000000 438350.000000	CNS E18 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	46	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel CNS E18 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel CNS E18 + 2\
subGroups view=PlusRawSignal age=E18 cellType=CNS rep=rep2\
track wgEncodeCshlLongRnaSeqCnsE18PlusRawRep2\
type bigWig 1.000000 438350.000000\

wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6MinusRawRep1	FatPad 8w MR 1	bigWig 1.000000 380134.000000	FatPad Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	46	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel FatPad Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel FatPad 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=FAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 380134.000000\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hSigRep1	G1E-ER GATA1 24hr	bigWig 1.000000 166.000000	G1E-ER4 GATA1 Estradiol 24 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	46	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 24 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER GATA1 24hr\
subGroups view=Signal age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=eDIFFD24H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd24hSigRep1\
type bigWig 1.000000 166.000000\
viewLimits 1:30\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hPlusRawRep2	G1E-ER4 3hr P 2	bigWig 1.000000 1022279.000000	G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	46	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 3hr P 2\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=cDIFFD3H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hPlusRawRep2\
type bigWig 1.000000 1022279.000000\

wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdPk	Liver 8w CTCF	broadPeak	Liver Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	46	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks\
shortLabel Liver 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep2	Liver 8wk Sg 2	bigWig 3.000000 65498.000000	Liver Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	46	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel Liver 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqLiverCellPapMAdult8wksC57bl6SigRep2\
type bigWig 3.000000 65498.000000\

wgEncodePsuHistoneMegakaryoH3k04me1BE14halfCd1InputSig	Megakary H3K4m1	bigWig 1.000000 480.000000	Megakaryocyte H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	46	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Megakary H3K4m1\
subGroups view=Signal age=E14HALF factor=H3K04ME1 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k04me1BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:250\

wgEncodeUwDgfNih3t3NihsMImmortalPkRep1	NIH-3T3 Immt P	narrowPeak	NIH-3T3 Immortal NIH/Swiss DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	46	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel NIH-3T3 Immortal NIH/Swiss DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel NIH-3T3 Immt P\
subGroups view=Peaks age=IMMORTAL cellType=NIH3T3 strain=NIHS treatment=NONE rep=rep1\
track wgEncodeUwDgfNih3t3NihsMImmortalPkRep1\
type narrowPeak\

wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xSigRep1	C2 SRF 24h 1	bigWig 0.048900 819.985291	C2C12 SRF Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	47	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 SRF Myocyte 24h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 SRF 24h 1\
subGroups view=Signal factor=SRF cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P24H rep=rep1\
track wgEncodeCaltechTfbsC2c12SrfFCntrl32bE2p24hPcr2xSigRep1\
type bigWig 0.048900 819.985291\

wgEncodeLicrHistoneCh12H3k36me3FImmortalC57bl6StdSig	CH12 H3K36m3	bigWig 0.120000 18.580000	CH12 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	47	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel CH12 H3K36m3\
subGroups view=Signal age=IMMORTAL factor=H3K36ME3 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k36me3FImmortalC57bl6StdSig\
type bigWig 0.120000 18.580000\
viewLimits 0.2:2\

wgEncodeUwDnaseCh122a4bFImmortalPkRep2	CH12 P 2	narrowPeak	CH12 DNaseI HS Peaks Rep 2 from ENCODE/UW	3	47	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel CH12 P 2\
subGroups view=Peaks age=IMMORTAL cellType=CH12 sex=F strain=b2A4B treatment=zNONE rep=rep2\
track wgEncodeUwDnaseCh122a4bFImmortalPkRep2\
type narrowPeak\

wgEncodeSydhTfbsCh12Ubfsc13125IggrabPk	CH12 UBF_s	narrowPeak	CH12 UBF (sc-13125) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	47	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 UBF (sc-13125) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 UBF_s\
subGroups view=Peaks factor=UBFSC13125 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Ubfsc13125IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCnsE18Contigs	CNS E18 C	bed 6 +	CNS E18 Long RNA-seq Contigs from ENCODE/CSHL	3	47	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E18 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel CNS E18 C\
subGroups view=Contigs age=E18 cellType=CNS rep=repP\
track wgEncodeCshlLongRnaSeqCnsE18Contigs\
type bed 6 +\

wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6PlusRawRep1	FatPad 8w PR 1	bigWig 1.000000 117369.000000	FatPad Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	47	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel FatPad Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel FatPad 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=FAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 117369.000000\

wgEncodePsuTfbsG1eer4InputME0S129InputDiffd24hSigRep1	G1E-ER Input 24hr	bigWig 1.000000 120.000000	G1E-ER4 Input Estradiol 24 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	47	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Input Estradiol 24 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER Input 24hr\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=eDIFFD24H rep=rep1\
track wgEncodePsuTfbsG1eer4InputME0S129InputDiffd24hSigRep1\
type bigWig 1.000000 120.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hMinusRawRep2	G1E-ER4 3hr M 2	bigWig -2055533.000000 -1.000000	G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	47	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 3hr M 2\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=cDIFFD3H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hMinusRawRep2\
type bigWig -2055533.000000 -1.000000\

wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdSig	Liver 8w CTCF	bigWig 0.110000 52.470001	Liver Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	47	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal\
shortLabel Liver 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLiverCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.110000 52.470001\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep1	Liver E14.5 Sg 1	bigWig 0.000000 65448.000000	Liver Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR	2	47	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Liver E14.5 Sg 1\
subGroups view=Signal age=E14HALF cellType=LIVER localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep1\
type bigWig 0.000000 65448.000000\

wgEncodePsuHistoneMegakaryoH3k04me3BE14halfCd1InputPk	Megakary H3K4m3	broadPeak	Megakaryocyte H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	47	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryocyte H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Megakary H3K4m3\
subGroups view=Peaks age=E14HALF factor=H3K04ME3 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k04me3BE14halfCd1InputPk\
type broadPeak\

wgEncodeUwDgfNih3t3NihsMImmortalRawRep1	NIH-3T3 Immt R	bigWig 1.000000 730682.000000	NIH-3T3 Immortal NIH/Swiss DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	47	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 Immortal NIH/Swiss DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel NIH-3T3 Immt R\
subGroups view=RawSignal age=IMMORTAL cellType=NIH3T3 strain=NIHS treatment=NONE rep=rep1\
track wgEncodeUwDgfNih3t3NihsMImmortalRawRep1\
type bigWig 1.000000 730682.000000\

wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xPkRep1	C2 TCF12 60h 1	narrowPeak	C2C12 TCF12 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	48	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 TCF12 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 TCF12 60h 1\
subGroups view=Peaks factor=TCF12 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xPkRep1\
type narrowPeak\

wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdPk	CH12 H3K79m2	broadPeak	CH12 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	48	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel CH12 H3K79m2\
subGroups view=Peaks age=IMMORTAL factor=H3K79ME2 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseCh122a4bFImmortalSigRep2	CH12 S 2	bigWig 1.000000 44111.000000	CH12 DNaseI HS Signal Rep 2 from ENCODE/UW	2	48	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel CH12 S 2\
subGroups view=Signal age=IMMORTAL cellType=CH12 sex=F strain=b2A4B treatment=zNONE rep=rep2\
track wgEncodeUwDnaseCh122a4bFImmortalSigRep2\
type bigWig 1.000000 44111.000000\

wgEncodeSydhTfbsCh12Ubfsc13125IggrabSig	CH12 UBF_s	bigWig 1.000000 90667.000000	CH12 UBF (sc-13125) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	48	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 UBF (sc-13125) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 UBF_s\
subGroups view=Signal factor=UBFSC13125 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Ubfsc13125IggrabSig\
type bigWig 1.000000 90667.000000\

wgEncodeCshlLongRnaSeqCnsE18Junctions	CNS E18 J	bed 6 +	CNS E18 Long RNA-seq Junctions from ENCODE/CSHL	0	48	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel CNS E18 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel CNS E18 J\
subGroups view=SJunctions age=E18 cellType=CNS rep=repP\
track wgEncodeCshlLongRnaSeqCnsE18Junctions\
type bed 6 +\

wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6SigRep1	FatPad 8w S 1	bigWig 1.000000 380134.000000	FatPad Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	48	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel FatPad Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel FatPad 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=FAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqFatCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 380134.000000\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hPkRep1	G1E-ER GATA1 30hr	broadPeak	G1E-ER4 GATA1 Estradiol 30 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU	3	48	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 30 hr TC TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel G1E-ER GATA1 30hr\
subGroups view=Peaks age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=fDIFFD30H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hPkRep1\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hAlnRep2	G1E-ER4 3hr A 2	bam	G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU	0	48	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 3 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 3hr A 2\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=cDIFFD3H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd3hAlnRep2\
type bam\

wgEncodeLicrTfbsLiverInputMAdult8wksC57bl6StdSig	Liver 8w Input	bigWig 0.130000 65.070000	Liver Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	48	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Liver 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLiverInputMAdult8wksC57bl6StdSig\
type bigWig 0.130000 65.070000\

wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep2	Liver E14.5 Sg 2	bigWig 0.000000 65468.000000	Liver Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR	2	48	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Liver E14.5 Sg 2\
subGroups view=Signal age=E14HALF cellType=LIVER localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqLiverCellPapUE14halfC57bl6SigRep2\
type bigWig 0.000000 65468.000000\

wgEncodePsuHistoneMegakaryoH3k04me3BE14halfCd1InputSig	Megakary H3K4m3	bigWig 1.000000 480.000000	Megakaryocyte H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	48	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Megakary H3K4m3\
subGroups view=Signal age=E14HALF factor=H3K04ME3 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k04me3BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:500\

wgEncodeUwDgfNih3t3NihsMImmortalSigRep1	NIH-3T3 Immt S	bigWig 1.000000 114005.000000	NIH-3T3 Immortal NIH/Swiss DNaseI DGF Signal Rep 1 from ENCODE/UW	2	48	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 Immortal NIH/Swiss DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel NIH-3T3 Immt S\
subGroups view=Signal age=IMMORTAL cellType=NIH3T3 strain=NIHS treatment=NONE rep=rep1\
track wgEncodeUwDgfNih3t3NihsMImmortalSigRep1\
type bigWig 1.000000 114005.000000\

wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xSigRep1	C2 TCF12 60h 1	bigWig 0.051800 6948.665527	C2C12 TCF12 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	49	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 TCF12 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 TCF12 60h 1\
subGroups view=Signal factor=TCF12 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Tcf12FCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.051800 6948.665527\

wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdSig	CH12 H3K79m2	bigWig 0.140000 89.820000	CH12 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	49	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel CH12 H3K79m2\
subGroups view=Signal age=IMMORTAL factor=H3K79ME2 cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12H3k79me2FImmortalC57bl6StdSig\
type bigWig 0.140000 89.820000\
viewLimits 0.2:3\

wgEncodeSydhTfbsCh12Usf2IggmusPk	CH12 USF2	narrowPeak	CH12 USF2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	49	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 USF2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 USF2\
subGroups view=Peaks factor=USF2 cellType=CH12 control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsCh12Usf2IggmusPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep1V2	Colon Aln 1	bam	Colon A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	49	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Colon A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Colon Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=COLON rep=rep1\
track wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep1V2\
type bam\

wgEncodeUwDnaseEpcmppCd1ME14halfHotspotsRep1	EPC -++ H 1	broadPeak	EPC (CD117-,CD71+,TER119+) DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	49	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel EPC (CD117-,CD71+,TER119+) DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel EPC -++ H 1\
subGroups view=Hotspots age=E14HALF cellType=EPCMPP sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcmppCd1ME14halfHotspotsRep1\
type broadPeak\

wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hSigRep1	G1E-ER GATA1 30hr	bigWig 1.000000 230.000000	G1E-ER4 GATA1 Estradiol 30 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	49	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 GATA1 Estradiol 30 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER GATA1 30hr\
subGroups view=Signal age=E0 factor=GATA1a cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=fDIFFD30H rep=rep1\
track wgEncodePsuTfbsG1eer4Gata1aME0S129InputDiffd30hSigRep1\
type bigWig 1.000000 230.000000\
viewLimits 1:100\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep1	G1E-ER4 7hr P 1	bigWig 1.000000 1100778.000000	G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	49	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 7hr P 1\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=dDIFFD7H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep1\
type bigWig 1.000000 1100778.000000\

wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep1	GenitalFP 8w A 1	bam	GenitalFatPad Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	49	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel GenitalFatPad Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel GenitalFP 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=GFAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeLicrTfbsLiverInputUE14halfC57bl6StdSig	Liver 14.5 Input	bigWig 0.130000 48.360001	Liver Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR	2	49	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Liver 14.5 Input\
subGroups view=Signal age=E14HALF factor=INPUT cellType=LIVER control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsLiverInputUE14halfC57bl6StdSig\
type bigWig 0.130000 48.360001\

wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep1	Lung 8wk Al 1	bam	Lung Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	49	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Lung 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=LUNG localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodePsuHistoneMegakaryoH3k09me3BE14halfCd1InputPk	Megakary H3K9m3	broadPeak	Megakaryocyte H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	49	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryocyte H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Megakary H3K9m3\
subGroups view=Peaks age=E14HALF factor=H3K09ME3 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k09me3BE14halfCd1InputPk\
type broadPeak\

wgEncodeUwDgfRetinaC57bl6MNew1daysHotspotsRep1	Retina 1day H	broadPeak	Retina Newborn 1 Day C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	49	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Retina Newborn 1 Day C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel Retina 1day H\
subGroups view=Hotspots age=NEW1DAYS cellType=RETINA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfRetinaC57bl6MNew1daysHotspotsRep1\
type broadPeak\

wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xPkRep1	C2 TCF3 5d 1	narrowPeak	C2C12 TCF3 Myocyte 5d TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	50	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 TCF3 Myocyte 5d TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 TCF3 5d 1\
subGroups view=Peaks factor=TCF3 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P5D rep=rep1\
track wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xPkRep1\
type narrowPeak\

wgEncodeLicrHistoneCh12InputFImmortalC57bl6StdSig	CH12 Input	bigWig 0.130000 39.959999	CH12 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	50	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel CH12 Input\
subGroups view=Signal age=IMMORTAL factor=INPUT cellType=CH12 control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistoneCh12InputFImmortalC57bl6StdSig\
type bigWig 0.130000 39.959999\
viewLimits 0.2:5\

wgEncodeSydhTfbsCh12Usf2IggmusSig	CH12 USF2	bigWig 1.000000 126147.000000	CH12 USF2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	50	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 USF2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 USF2\
subGroups view=Signal factor=USF2 cellType=CH12 control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsCh12Usf2IggmusSig\
type bigWig 1.000000 126147.000000\

wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep1	Colon - 1	bigWig 1.000000 295940.000000	Colon A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	50	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Colon A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Colon - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=COLON rep=rep1\
track wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep1\
type bigWig 1.000000 295940.000000\

wgEncodeUwDnaseEpcmppCd1ME14halfPkRep1	EPC -++ P 1	narrowPeak	EPC (CD117-,CD71+,TER119+) DNaseI HS Peaks Rep 1 from ENCODE/UW	3	50	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel EPC (CD117-,CD71+,TER119+) DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel EPC -++ P 1\
subGroups view=Peaks age=E14HALF cellType=EPCMPP sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcmppCd1ME14halfPkRep1\
type narrowPeak\

wgEncodePsuTfbsG1eer4InputME0S129InputDiffd30hSigRep1	G1E-ER Input 30hr	bigWig 1.000000 114.000000	G1E-ER4 Input Estradiol 30 hr TC TFBS ChIP-seq Signal from ENCODE/PSU	2	50	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Input Estradiol 30 hr TC TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel G1E-ER Input 30hr\
subGroups view=Signal age=E0 factor=zINPUT cellType=G1EER4T control=INPUT sex=M strain=s129 treatment=fDIFFD30H rep=rep1\
track wgEncodePsuTfbsG1eer4InputME0S129InputDiffd30hSigRep1\
type bigWig 1.000000 114.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep1	G1E-ER4 7hr M 1	bigWig -979957.000000 -1.000000	G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	50	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 7hr M 1\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=dDIFFD7H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep1\
type bigWig -979957.000000 -1.000000\

wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep2	GenitalFP 8w A 2	bam	GenitalFatPad Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW	0	50	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel GenitalFatPad Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel GenitalFP 8w A 2\
subGroups view=Alignments age=ADULT8WKS cellType=GFAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdPk	Liver 8w Pol2	broadPeak	Liver Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	50	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks\
shortLabel Liver 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep2	Lung 8wk Al 2	bam	Lung Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	50	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Lung 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=LUNG localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodePsuHistoneMegakaryoH3k09me3BE14halfCd1InputSig	Megakary H3K9m3	bigWig 1.000000 480.000000	Megakaryocyte H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	50	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Megakary H3K9m3\
subGroups view=Signal age=E14HALF factor=H3K09ME3 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k09me3BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:200\

wgEncodeUwDgfRetinaC57bl6MNew1daysPkRep1	Retina 1day P	narrowPeak	Retina Newborn 1 Day C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	50	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Retina Newborn 1 Day C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel Retina 1day P\
subGroups view=Peaks age=NEW1DAYS cellType=RETINA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfRetinaC57bl6MNew1daysPkRep1\
type narrowPeak\

wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xSigRep1	C2 TCF3 5d 1	bigWig 0.077000 986.911194	C2C12 TCF3 Myocyte 5d TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	51	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 TCF3 Myocyte 5d TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 TCF3 5d 1\
subGroups view=Signal factor=TCF3 cellType=C2C12 control=CNTRL32B protocol=PCR2X sex=F treatment=E2P5D rep=rep1\
track wgEncodeCaltechTfbsC2c12Tcf3FCntrl32bE2p5dPcr2xSigRep1\
type bigWig 0.077000 986.911194\

wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabPk	CH12 ZC3H11A P	narrowPeak	CH12 ZC3H11A (NB100-74650) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	51	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 ZC3H11A (NB100-74650) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 ZC3H11A P\
subGroups view=Peaks factor=ZC3H11ANB10074650 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep1	Colon + 1	bigWig 1.000000 935051.000000	Colon A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	51	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Colon A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Colon + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=COLON rep=rep1\
track wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep1\
type bigWig 1.000000 935051.000000\

wgEncodeLicrHistoneCortexH3k4me1MAdult8wksC57bl6StdPk	Cortex H3K4m1	broadPeak	Cortex 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	51	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Cortex H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCortexH3k4me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseEpcmppCd1ME14halfSigRep1	EPC -++ S 1	bigWig 1.000000 99568.000000	EPC (CD117-,CD71+,TER119+) DNaseI HS Signal Rep 1 from ENCODE/UW	2	51	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel EPC (CD117-,CD71+,TER119+) DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel EPC -++ S 1\
subGroups view=Signal age=E14HALF cellType=EPCMPP sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcmppCd1ME14halfSigRep1\
type bigWig 1.000000 99568.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hAlnRep1	G1E-ER4 7hr A 1	bam	G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU	0	51	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 7hr A 1\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=dDIFFD7H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hAlnRep1\
type bam\

wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep1	GenitalFP 8w MR 1	bigWig 1.000000 1643654.000000	GenitalFatPad Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	51	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel GenitalFatPad Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel GenitalFP 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=GFAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 1643654.000000\

wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdSig	Liver 8w Pol2	bigWig 0.160000 45.200001	Liver Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	51	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal\
shortLabel Liver 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLiverPol2MAdult8wksC57bl6StdSig\
type bigWig 0.160000 45.200001\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep1	Lung 8wk Sg 1	bigWig 4.000000 65435.000000	Lung Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	51	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Lung 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=LUNG localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep1\
type bigWig 4.000000 65435.000000\

wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputPk	Megakary FLI1	broadPeak	Megakaryo FLI1 TFBS ChIP-seq Peaks from ENCODE/PSU	3	51	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryo FLI1 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks\
shortLabel Megakary FLI1\
subGroups view=Peaks age=E14HALF factor=FLI1SC356 cellType=MEGAKARYO control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputPk\
type broadPeak\

wgEncodePsuHistoneMegakaryoH3k27me3BE14halfCd1InputPk	Megakary H3K27m3	broadPeak	Megakaryocyte H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	51	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryocyte H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Megakary H3K27m3\
subGroups view=Peaks age=E14HALF factor=H3K27ME3 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k27me3BE14halfCd1InputPk\
type broadPeak\

wgEncodeUwDgfRetinaC57bl6MNew1daysRawRep1	Retina 1day R	bigWig 1.000000 882041.000000	Retina Newborn 1 Day C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	51	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Retina Newborn 1 Day C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel Retina 1day R\
subGroups view=RawSignal age=NEW1DAYS cellType=RETINA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfRetinaC57bl6MNew1daysRawRep1\
type bigWig 1.000000 882041.000000\

wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xPkRep1	C2 USF-1 60h 1	narrowPeak	C2C12 USF-1 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	52	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 USF-1 Myocyte 60h TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 USF-1 60h 1\
subGroups view=Peaks factor=USF1 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xPkRep1\
type narrowPeak\

wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabSig	CH12 ZC3H11A S	bigWig 1.000000 72717.000000	CH12 ZC3H11A (NB100-74650) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	52	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 ZC3H11A (NB100-74650) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 ZC3H11A S\
subGroups view=Signal factor=ZC3H11ANB10074650 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Zc3h11anb10074650IggrabSig\
type bigWig 1.000000 72717.000000\

wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep2V2	Colon Aln 2	bam	Colon A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	52	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Colon A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Colon Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=COLON rep=rep2\
track wgEncodeCshlLongRnaSeqColonAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistoneCortexH3k4me1MAdult8wksC57bl6StdSig	Cortex H3K4m1	bigWig 0.110000 8.410000	Cortex 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	52	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Cortex H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCortexH3k4me1MAdult8wksC57bl6StdSig\
type bigWig 0.110000 8.410000\
viewLimits 0.2:3\

wgEncodeUwDnaseEpcpmmCd1ME14halfHotspotsRep1	EPC +-- H 1	broadPeak	EPC (CD117+,CD71-,TER119-) DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	52	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel EPC (CD117+,CD71-,TER119-) DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel EPC +-- H 1\
subGroups view=Hotspots age=E14HALF cellType=EPCPMM sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcpmmCd1ME14halfHotspotsRep1\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep2	G1E-ER4 7hr P 2	bigWig 1.000000 1463770.000000	G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	52	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 7hr P 2\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=dDIFFD7H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hPlusRawRep2\
type bigWig 1.000000 1463770.000000\

wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep2	GenitalFP 8w MR 2	bigWig 1.000000 145604.000000	GenitalFatPad Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	52	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel GenitalFatPad Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel GenitalFP 8w MR 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=GFAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6MinusRawRep2\
type bigWig 1.000000 145604.000000\

wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdPk	Lung 8w CTCF	broadPeak	Lung Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	52	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Lung 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep2	Lung 8wk Sg 2	bigWig 4.000000 65503.000000	Lung Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	52	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Lung 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=LUNG localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqLungCellPapMAdult8wksC57bl6SigRep2\
type bigWig 4.000000 65503.000000\

wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputSig	Megakary FLI1	bigWig 1.000000 114.000000	Megakaryocyte FLI1 TFBS ChIP-seq Signal from ENCODE/PSU	2	52	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte FLI1 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal\
shortLabel Megakary FLI1\
subGroups view=Signal age=E14HALF factor=FLI1SC356 cellType=MEGAKARYO control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsMegakaryoFli1sc356BE14halfCd1InputSig\
type bigWig 1.000000 114.000000\

wgEncodePsuHistoneMegakaryoH3k27me3BE14halfCd1InputSig	Megakary H3K27m3	bigWig 1.000000 480.000000	Megakaryocyte H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	52	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Megakary H3K27m3\
subGroups view=Signal age=E14HALF factor=H3K27ME3 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k27me3BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:300\

wgEncodeUwDgfRetinaC57bl6MNew1daysSigRep1	Retina 1day S	bigWig 1.000000 112503.000000	Retina Newborn 1 Day C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	52	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Retina Newborn 1 Day C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel Retina 1day S\
subGroups view=Signal age=NEW1DAYS cellType=RETINA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfRetinaC57bl6MNew1daysSigRep1\
type bigWig 1.000000 112503.000000\

wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xSigRep1	C2 USF-1 60h 1	bigWig 0.047700 11492.834961	C2C12 USF-1 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	53	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 USF-1 Myocyte 60h TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 USF-1 60h 1\
subGroups view=Signal factor=USF1 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=E2P60H rep=rep1\
track wgEncodeCaltechTfbsC2c12Usf1FCntrl50bE2p60hPcr1xSigRep1\
type bigWig 0.047700 11492.834961\

wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabPk	CH12 ZKSCAN1_H	narrowPeak	CH12 ZKSCAN1 (HPA006672) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	53	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 ZKSCAN1 (HPA006672) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 ZKSCAN1_H\
subGroups view=Peaks factor=ZKSCAN1HPA006672 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep2	Colon - 2	bigWig 1.000000 432217.000000	Colon A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	53	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Colon A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Colon - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=COLON rep=rep2\
track wgEncodeCshlLongRnaSeqColonAdult8wksMinusRawRep2\
type bigWig 1.000000 432217.000000\

wgEncodeLicrHistoneCortexH3k4me3MAdult8wksC57bl6StdPk	Cortex H3K4m3	broadPeak	Cortex 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	53	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Cortex H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCortexH3k4me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseEpcpmmCd1ME14halfPkRep1	EPC +-- P 1	narrowPeak	EPC (CD117+,CD71-,TER119-) DNaseI HS Peaks Rep 1 from ENCODE/UW	3	53	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel EPC (CD117+,CD71-,TER119-) DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel EPC +-- P 1\
subGroups view=Peaks age=E14HALF cellType=EPCPMM sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcpmmCd1ME14halfPkRep1\
type narrowPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep2	G1E-ER4 7hr M 2	bigWig -2091379.000000 -1.000000	G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	53	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 7hr M 2\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=dDIFFD7H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hMinusRawRep2\
type bigWig -2091379.000000 -1.000000\

wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep1	GenitalFP 8w PR 1	bigWig 1.000000 1726627.000000	GenitalFatPad Adult 8 weeks RNA-seq Plus Raw signal Rep 1 from ENCODE/UW	2	53	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel GenitalFatPad Adult 8 weeks RNA-seq Plus Raw signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel GenitalFP 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=GFAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 1726627.000000\

wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdSig	Lung 8w CTCF	bigWig 0.160000 34.049999	Lung Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	53	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Lung 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLungCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.160000 34.049999\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep1	MEF 8wk Al 1	bam	MEF Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	53	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel MEF Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel MEF 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=MEF localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputPkV2	Megakary GATA1	broadPeak	Megakaryocyte GATA1 TFBS ChIP-seq Peaks from ENCODE/PSU	3	53	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryocyte GATA1 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks\
shortLabel Megakary GATA1\
subGroups view=Peaks age=E14HALF factor=GATA1a cellType=MEGAKARYO control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputPkV2\
type broadPeak\

wgEncodePsuHistoneMegakaryoH3k36me3BE14halfCd1InputPk	Megakary H3K36m3	broadPeak	Megakaryocyte H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU	3	53	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryocyte H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuHistoneViewPeaks\
shortLabel Megakary H3K36m3\
subGroups view=Peaks age=E14HALF factor=H3K36ME3 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k36me3BE14halfCd1InputPk\
type broadPeak\

wgEncodeUwDgfThelpaC57bl6MAdult8wksHotspotsRep1	THelp-Act 8w H	broadPeak	THelper-Activated 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	53	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel THelper-Activated 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel THelp-Act 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=THELPA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfThelpaC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xPkRep1	C2 USF-1 1	narrowPeak	C2C12 USF-1 Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech	3	54	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel C2C12 USF-1 Myoblast TFBS ChIP-seq Peaks Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewPeaks off\
shortLabel C2 USF-1 1\
subGroups view=Peaks factor=USF1 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xPkRep1\
type narrowPeak\

wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabSig	CH12 ZKSCAN1_H	bigWig 1.000000 79290.000000	CH12 ZKSCAN1 (HPA006672) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	54	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 ZKSCAN1 (HPA006672) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 ZKSCAN1_H\
subGroups view=Signal factor=ZKSCAN1HPA006672 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Zkscan1hpa006672IggrabSig\
type bigWig 1.000000 79290.000000\

wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep2	Colon + 2	bigWig 1.000000 725162.000000	Colon A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	54	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Colon A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Colon + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=COLON rep=rep2\
track wgEncodeCshlLongRnaSeqColonAdult8wksPlusRawRep2\
type bigWig 1.000000 725162.000000\

wgEncodeLicrHistoneCortexH3k4me3MAdult8wksC57bl6StdSig	Cortex H3K4m3	bigWig 0.110000 44.410000	Cortex 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	54	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Cortex H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCortexH3k4me3MAdult8wksC57bl6StdSig\
type bigWig 0.110000 44.410000\
viewLimits 0.2:10\

wgEncodeUwDnaseEpcpmmCd1ME14halfSigRep1	EPC +-- S 1	bigWig 1.000000 56275.000000	EPC (CD117+,CD71-,TER119-) DNaseI HS Signal Rep 1 from ENCODE/UW	2	54	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel EPC (CD117+,CD71-,TER119-) DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel EPC +-- S 1\
subGroups view=Signal age=E14HALF cellType=EPCPMM sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcpmmCd1ME14halfSigRep1\
type bigWig 1.000000 56275.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hAlnRep2	G1E-ER4 7hr A 2	bam	G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU	0	54	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 7 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 7hr A 2\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=dDIFFD7H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd7hAlnRep2\
type bam\

wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep2	GenitalFP 8w PR 2	bigWig 1.000000 145542.000000	GenitalFatPad Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	54	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel GenitalFatPad Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel GenitalFP 8w PR 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=GFAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6PlusRawRep2\
type bigWig 1.000000 145542.000000\

wgEncodeLicrTfbsLungInputMAdult8wksC57bl6StdSig	Lung 8w Input	bigWig 0.150000 39.330002	Lung Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	54	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Lung 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLungInputMAdult8wksC57bl6StdSig\
type bigWig 0.150000 39.330002\

wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep2	MEF 8wk Al 2	bam	MEF Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	54	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel MEF Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel MEF 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=MEF localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputSigV2	Megakary GATA1	bigWig 1.000000 102.000000	Megakaryocyte GATA1 TFBS ChIP-seq Signal from ENCODE/PSU	2	54	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte GATA1 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal\
shortLabel Megakary GATA1\
subGroups view=Signal age=E14HALF factor=GATA1a cellType=MEGAKARYO control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsMegakaryoGata1aBE14halfCd1InputSigV2\
type bigWig 1.000000 102.000000\

wgEncodePsuHistoneMegakaryoH3k36me3BE14halfCd1InputSig	Megakary H3K36m3	bigWig 1.000000 480.000000	Megakaryocyte H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	54	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal\
shortLabel Megakary H3K36m3\
subGroups view=Signal age=E14HALF factor=H3K36ME3 cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoH3k36me3BE14halfCd1InputSig\
type bigWig 1.000000 480.000000\
viewLimits 2:300\

wgEncodeUwDgfThelpaC57bl6MAdult8wksPkRep1	THelp-Act 8w P	narrowPeak	THelper-Activated 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	54	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel THelper-Activated 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel THelp-Act 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=THELPA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfThelpaC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xSigRep1	C2 USF-1 1	bigWig 0.049600 10984.600586	C2C12 USF-1 Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech	2	55	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel C2C12 USF-1 Myoblast TFBS ChIP-seq Signal Rep 1 from ENCODE/Caltech\
parent wgEncodeCaltechTfbsViewSignal off\
shortLabel C2 USF-1 1\
subGroups view=Signal factor=USF1 cellType=C2C12 control=CNTRL50B protocol=PCR1X sex=F treatment=NONE rep=rep1\
track wgEncodeCaltechTfbsC2c12Usf1FCntrl50bPcr1xSigRep1\
type bigWig 0.049600 10984.600586\

wgEncodeSydhTfbsCh12Znf384hpa004051IggrabPk	CH12 ZNF384 P	narrowPeak	CH12 ZNF384 (HPA004051) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	55	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 ZNF384 (HPA004051) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 ZNF384 P\
subGroups view=Peaks factor=ZNF384HPA004051 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Znf384hpa004051IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqColonAdult8wksContigs	Colon C	bed 6 +	Colon A8 Long RNA-seq Contigs from ENCODE/CSHL	3	55	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Colon A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Colon C\
subGroups view=Contigs age=ADULT8WKS cellType=COLON rep=repP\
track wgEncodeCshlLongRnaSeqColonAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneCortexH3k27acMAdult8wksC57bl6StdPk	Cortex H3K27a	broadPeak	Cortex 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	55	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Cortex H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCortexH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseEpcppmCd1ME14halfHotspotsRep1	EPC ++- H 1	broadPeak	EPC (CD117+,CD71+,TER119-) DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	55	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel EPC (CD117+,CD71+,TER119-) DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel EPC ++- H 1\
subGroups view=Hotspots age=E14HALF cellType=EPCPPM sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcppmCd1ME14halfHotspotsRep1\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hPlusRawRep1	G1E-ER4 14hr P 1	bigWig 1.000000 1384730.000000	G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	55	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 14hr P 1\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=eDIFFD14H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hPlusRawRep1\
type bigWig 1.000000 1384730.000000\

wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep1	GenitalFP 8w S 1	bigWig 1.000000 1726627.000000	GenitalFatPad Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	55	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel GenitalFatPad Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel GenitalFP 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=GFAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 1726627.000000\

wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdPk	Lung 8w Pol2	broadPeak	Lung Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	55	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Lung 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep1	MEF 8wk Sg 1	bigWig 4.000000 65454.000000	MEF Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	55	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel MEF 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=MEF localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep1\
type bigWig 4.000000 65454.000000\

wgEncodePsuHistoneMegakaryoInputBE14halfCd1InputSig	Megakary Input	bigWig 1.000000 128.000000	Megakaryocyte Input Histone Mods by ChIP-seq Signal from ENCODE/PSU	2	55	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte Input Histone Mods by ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuHistoneViewSignal off\
shortLabel Megakary Input\
subGroups view=Signal age=E14HALF factor=zINPUT cellType=MEGAKARYO control=INPUT treatment=aNONE sex=B strain=CD1\
track wgEncodePsuHistoneMegakaryoInputBE14halfCd1InputSig\
type bigWig 1.000000 128.000000\

wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputPk	Megakary TAL1	broadPeak	Megakaryocyte TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU	3	55	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryocyte TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks\
shortLabel Megakary TAL1\
subGroups view=Peaks age=E14HALF factor=TAL1 cellType=MEGAKARYO control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputPk\
type broadPeak\

wgEncodeUwDgfThelpaC57bl6MAdult8wksRawRep1	THelp-Act 8w R	bigWig 1.000000 708959.000000	THelper-Activated 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	55	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel THelper-Activated 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel THelp-Act 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=THELPA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfThelpaC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 708959.000000\

wgEncodeSydhTfbsCh12Znf384hpa004051IggrabSig	CH12 ZNF384 S	bigWig 1.000000 50168.000000	CH12 ZNF384 (HPA004051) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	56	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 ZNF384 (HPA004051) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 ZNF384 S\
subGroups view=Signal factor=ZNF384HPA004051 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Znf384hpa004051IggrabSig\
type bigWig 1.000000 50168.000000\

wgEncodeCshlLongRnaSeqColonAdult8wksJunctions	Colon J	bed 6 +	Colon A8 Long RNA-seq Junctions from ENCODE/CSHL	0	56	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Colon A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Colon J\
subGroups view=SJunctions age=ADULT8WKS cellType=COLON rep=repP\
track wgEncodeCshlLongRnaSeqColonAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneCortexH3k27acMAdult8wksC57bl6StdSig	Cortex H3K27a	bigWig 0.140000 26.379999	Cortex 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	56	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Cortex H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCortexH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.140000 26.379999\
viewLimits 0.2:5\

wgEncodeUwDnaseEpcppmCd1ME14halfPkRep1	EPC ++- P 1	narrowPeak	EPC (CD117+,CD71+,TER119-) DNaseI HS Peaks Rep 1 from ENCODE/UW	3	56	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel EPC (CD117+,CD71+,TER119-) DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel EPC ++- P 1\
subGroups view=Peaks age=E14HALF cellType=EPCPPM sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcppmCd1ME14halfPkRep1\
type narrowPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hMinusRawRep1	G1E-ER4 14hr M 1	bigWig -2862238.000000 -1.000000	G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	56	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 14hr M 1\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=eDIFFD14H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hMinusRawRep1\
type bigWig -2862238.000000 -1.000000\

wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep2	GenitalFP 8w S 2	bigWig 1.000000 145608.000000	GenitalFatPad Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW	2	56	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel GenitalFatPad Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel GenitalFP 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=GFAT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqGfatCellPolyaMAdult8wksC57bl6SigRep2\
type bigWig 1.000000 145608.000000\

wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdSig	Lung 8w Pol2	bigWig 0.120000 48.990002	Lung Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	56	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Lung 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsLungPol2MAdult8wksC57bl6StdSig\
type bigWig 0.120000 48.990002\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep2	MEF 8wk Sg 2	bigWig 4.000000 65533.000000	MEF Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	56	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel MEF 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=MEF localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqMefCellPapMAdult8wksC57bl6SigRep2\
type bigWig 4.000000 65533.000000\

wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputSig	Megakary TAL1	bigWig 1.000000 154.000000	Megakaryocyte TAL1 TFBS ChIP-seq Signal from ENCODE/PSU	2	56	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte TAL1 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal\
shortLabel Megakary TAL1\
subGroups view=Signal age=E14HALF factor=TAL1 cellType=MEGAKARYO control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsMegakaryoTal1BE14halfCd1InputSig\
type bigWig 1.000000 154.000000\

wgEncodeUwDgfThelpaC57bl6MAdult8wksSigRep1	THelp-Act 8w S	bigWig 1.000000 184749.000000	THelper-Activated 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	56	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel THelper-Activated 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel THelp-Act 8w S\
subGroups view=Signal age=ADULT8WKS cellType=THELPA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfThelpaC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 184749.000000\

wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabPk	CH12 ZNF-MIZD P	narrowPeak	CH12 ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	57	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 ZNF-MIZD P\
subGroups view=Peaks factor=ZNFMIZDCP1AB65767 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep1	Cortex Aln 1	bam	Cortex A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	57	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Cortex Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=CORTEX rep=rep1\
track wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep1\
type bam\

wgEncodeLicrHistoneCortexInputMAdult8wksC57bl6StdSig	Cortex Input	bigWig 0.130000 61.080002	Cortex 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	57	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Cortex Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=CORTEX control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneCortexInputMAdult8wksC57bl6StdSig\
type bigWig 0.130000 61.080002\
viewLimits 0.2:5\

wgEncodeUwDnaseEpcppmCd1ME14halfSigRep1	EPC ++- S 1	bigWig 1.000000 55878.000000	EPC (CD117+,CD71+,TER119-) DNaseI HS Signal Rep 1 from ENCODE/UW	2	57	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel EPC (CD117+,CD71+,TER119-) DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel EPC ++- S 1\
subGroups view=Signal age=E14HALF cellType=EPCPPM sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcppmCd1ME14halfSigRep1\
type bigWig 1.000000 55878.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hAlnRep1	G1E-ER4 14hr A 1	bam	G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU	0	57	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 14hr A 1\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=eDIFFD14H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hAlnRep1\
type bam\

wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1AlnRep1	HlessE E11.5 A 1	bam	HeadlessEmbryo day 11.5 RNA-seq Alignments Rep 1 from ENCODE/UW	0	57	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel HeadlessEmbryo day 11.5 RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel HlessE E11.5 A 1\
subGroups view=Alignments age=E11HALF cellType=H1LEMBRYO localization=CELL rnaExtract=POLYA sex=M strain=CD1 rep=rep1\
track wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1AlnRep1\
type bam\

wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdPk	MEF 8w CTCF	broadPeak	MEF Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	57	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel MEF Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel MEF 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodePsuTfbsMegakaryoInputBE14halfCd1InputSig	Megakaryo Input	bigWig 1.000000 128.000000	Megakaryocyte Input TFBS ChIP-seq Signal from ENCODE/PSU	2	57	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte Input TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel Megakaryo Input\
subGroups view=Signal age=E14HALF factor=zINPUT cellType=MEGAKARYO control=INPUT treatment=aNONE rep=repP sex=B strain=CD1\
track wgEncodePsuTfbsMegakaryoInputBE14halfCd1InputSig\
type bigWig 1.000000 128.000000\

wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep1	MEL Al 1	bam	MEL Immortal cells RNA-seq Alignments Rep 1 from ENCODE/LICR	0	57	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Immortal cells RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel MEL Al 1\
subGroups view=Alignments age=IMMORTAL cellType=MEL localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep1\
type bam\

wgEncodeUwDgfThymusC57bl6MAdult8wksHotspotsRep1	Thymus 8w H	broadPeak	Thymus 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	57	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel Thymus 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=THYMUS strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfThymusC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabSig	CH12 ZNF-MIZD S	bigWig 1.000000 60293.000000	CH12 ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	58	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 ZNF-MIZD S\
subGroups view=Signal factor=ZNFMIZDCP1AB65767 cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12Znfmizdcp1ab65767IggrabSig\
type bigWig 1.000000 60293.000000\

wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep1	Cortex - 1	bigWig 1.000000 1004512.000000	Cortex A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	58	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Cortex - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=CORTEX rep=rep1\
track wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep1\
type bigWig 1.000000 1004512.000000\

wgEncodeUwDnaseEpcpppCd1ME14halfHotspotsRep1	EPC +++ H 1	broadPeak	EPC (CD117+,CD71+,TER119+) DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	58	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel EPC (CD117+,CD71+,TER119+) DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel EPC +++ H 1\
subGroups view=Hotspots age=E14HALF cellType=EPCPPP sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcpppCd1ME14halfHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneEsb4H3k4me1ME0C57bl6StdPk	ES-Bruce4 H3K4m1	broadPeak	ES-Bruce4 E0 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	58	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 E0 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-Bruce4 H3K4m1\
subGroups view=Peaks age=E0 factor=H3K04ME1 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k4me1ME0C57bl6StdPk\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hPlusRawRep2	G1E-ER4 14hr P 2	bigWig 1.000000 1053911.000000	G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	58	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 14hr P 2\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=eDIFFD14H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hPlusRawRep2\
type bigWig 1.000000 1053911.000000\

wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1MinusRawRep1	HlessE E11.5 MR 1	bigWig 1.000000 94576.000000	HeadlessEmbryo day 11.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	58	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel HeadlessEmbryo day 11.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel HlessE E11.5 MR 1\
subGroups view=MinusRawSignal age=E11HALF cellType=H1LEMBRYO localization=CELL rnaExtract=POLYA sex=M strain=CD1 rep=rep1\
track wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1MinusRawRep1\
type bigWig 1.000000 94576.000000\

wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdSig	MEF 8w CTCF	bigWig 0.160000 68.889999	MEF Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	58	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel MEF 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMefCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.160000 68.889999\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep2	MEL Al 2	bam	MEL Immortal cells RNA-seq Alignments Rep 2 from ENCODE/LICR	0	58	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Immortal cells RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel MEL Al 2\
subGroups view=Alignments age=IMMORTAL cellType=MEL localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6AlnRep2\
type bam\

wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputPk	MEL CTCF	broadPeak	MEL CTCF TFBS ChIP-seq Peaks from ENCODE/PSU	3	58	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL CTCF TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel MEL CTCF\
subGroups view=Peaks age=IMMORTAL factor=CTCF cellType=MEL control=INPUT treatment=aNONE rep=repP sex=M strain=C57BL6\
track wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputPk\
type broadPeak\

wgEncodeUwDgfThymusC57bl6MAdult8wksPkRep1	Thymus 8w P	narrowPeak	Thymus 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	58	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel Thymus 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=THYMUS strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfThymusC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeSydhTfbsCh12InputIggmusSig	CH12 IgG-mus	bigWig 1 71455	CH12 IgG-mus Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	59	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 IgG-mus Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 IgG-mus\
subGroups view=Signal factor=ZZZInputIGGMUS cellType=CH12 control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsCh12InputIggmusSig\
type bigWig 1 71455\

wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep1	Cortex + 1	bigWig 1.000000 1131486.000000	Cortex A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	59	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Cortex + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=CORTEX rep=rep1\
track wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep1\
type bigWig 1.000000 1131486.000000\

wgEncodeUwDnaseEpcpppCd1ME14halfPkRep1	EPC +++ P 1	narrowPeak	EPC (CD117+,CD71+,TER119+) DNaseI HS Peaks Rep 1 from ENCODE/UW	3	59	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel EPC (CD117+,CD71+,TER119+) DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel EPC +++ P 1\
subGroups view=Peaks age=E14HALF cellType=EPCPPP sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcpppCd1ME14halfPkRep1\
type narrowPeak\

wgEncodeLicrHistoneEsb4H3k4me1ME0C57bl6StdSig	ES-Bruce4 H3K4m1	bigWig 0.130000 38.650002	ES-Bruce4 E0 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	59	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 E0 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-Bruce4 H3K4m1\
subGroups view=Signal age=E0 factor=H3K04ME1 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k4me1ME0C57bl6StdSig\
type bigWig 0.130000 38.650002\
viewLimits 0.2:3\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hMinusRawRep2	G1E-ER4 14hr M 2	bigWig -1798329.000000 -1.000000	G1E-ER4 Estrdiol 14 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	59	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estrdiol 14 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 14hr M 2\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=eDIFFD14H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hMinusRawRep2\
type bigWig -1798329.000000 -1.000000\

wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1PlusRawRep1	HlessE E11.5 PR 1	bigWig 1.000000 57610.000000	HeadlessEmbryo day 11.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	59	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel HeadlessEmbryo day 11.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel HlessE E11.5 PR 1\
subGroups view=PlusRawSignal age=E11HALF cellType=H1LEMBRYO localization=CELL rnaExtract=POLYA sex=M strain=CD1 rep=rep1\
track wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1PlusRawRep1\
type bigWig 1.000000 57610.000000\

wgEncodeLicrTfbsMefInputMAdult8wksC57bl6StdSig	MEF 8w Input	bigWig 0.140000 50.770000	MEF Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	59	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel MEF 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMefInputMAdult8wksC57bl6StdSig\
type bigWig 0.140000 50.770000\

wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputSig	MEL CTCF	bigWig 1.000000 254.000000	MEL CTCF TFBS ChIP-seq Signal from ENCODE/PSU	2	59	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL CTCF TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel MEL CTCF\
subGroups view=Signal age=IMMORTAL factor=CTCF cellType=MEL control=INPUT treatment=aNONE rep=repP sex=M strain=C57BL6\
track wgEncodePsuTfbsMelCtcfMImmortalC57bl6InputSig\
type bigWig 1.000000 254.000000\
viewLimits 1:100\

wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep1	MEL Sg 1	bigWig 0.000000 65532.000000	MEL Immortal cells RNA-seq Signal Rep 1 from ENCODE/LICR	2	59	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal cells RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel MEL Sg 1\
subGroups view=Signal age=IMMORTAL cellType=MEL localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep1\
type bigWig 0.000000 65532.000000\

wgEncodeUwDgfThymusC57bl6MAdult8wksRawRep1	Thymus 8w R	bigWig 1.000000 609152.000000	Thymus 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	59	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel Thymus 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=THYMUS strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfThymusC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 609152.000000\

wgEncodeSydhTfbsCh12InputIggrabSig	CH12 IgG-rab	bigWig 1 66328	CH12 IgG-rab Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	60	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 IgG-rab Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 IgG-rab\
subGroups view=Signal factor=ZZZInputIGGRAB cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12InputIggrabSig\
type bigWig 1 66328\

wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep2	Cortex Aln 2	bam	Cortex A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	60	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Cortex Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=CORTEX rep=rep2\
track wgEncodeCshlLongRnaSeqCortexAdult8wksAlnRep2\
type bam\

wgEncodeUwDnaseEpcpppCd1ME14halfSigRep1	EPC +++ S 1	bigWig 1.000000 137727.000000	EPC (CD117+,CD71+,TER119+) DNaseI HS Signal Rep 1 from ENCODE/UW	2	60	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel EPC (CD117+,CD71+,TER119+) DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel EPC +++ S 1\
subGroups view=Signal age=E14HALF cellType=EPCPPP sex=M strain=CD1 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEpcpppCd1ME14halfSigRep1\
type bigWig 1.000000 137727.000000\

wgEncodeLicrHistoneEsb4H3k4me3ME0C57bl6StdPk	ES-Bruce4 H3K4m3	broadPeak	ES-Bruce4 E0 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	60	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 E0 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-Bruce4 H3K4m3\
subGroups view=Peaks age=E0 factor=H3K04ME3 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k4me3ME0C57bl6StdPk\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hAlnRep2	G1E-ER4 14hr A 2	bam	G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU	0	60	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 14 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 14hr A 2\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=eDIFFD14H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd14hAlnRep2\
type bam\

wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1SigRep1	HlessE E11.5 S 1	bigWig 1.000000 94576.000000	HeadlessEmbryo day 11.5 RNA-seq Signal Rep 1 from ENCODE/UW	2	60	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel HeadlessEmbryo day 11.5 RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel HlessE E11.5 S 1\
subGroups view=Signal age=E11HALF cellType=H1LEMBRYO localization=CELL rnaExtract=POLYA sex=M strain=CD1 rep=rep1\
track wgEncodeUwRnaSeqHlembryoCellPolyaME11halfCd1SigRep1\
type bigWig 1.000000 94576.000000\

wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdPk	MEF 8w Pol2	broadPeak	MEF Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	60	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel MEF Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel MEF 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputPk	MEL Pol2	broadPeak	MEL Pol2 TFBS ChIP-seq Peaks from ENCODE/PSU	3	60	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Pol2 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel MEL Pol2\
subGroups view=Peaks age=IMMORTAL factor=POL24H8 cellType=MEL control=INPUT treatment=aNONE rep=repP sex=M strain=C57BL6\
track wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputPk\
type broadPeak\

wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep2	MEL Sg 2	bigWig 0.000000 65495.000000	MEL Immortal cells RNA-seq Signal Rep 2 from ENCODE/LICR	2	60	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal cells RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel MEL Sg 2\
subGroups view=Signal age=IMMORTAL cellType=MEL localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqMelCellPapMImmortalC57bl6SigRep2\
type bigWig 0.000000 65495.000000\

wgEncodeUwDgfThymusC57bl6MAdult8wksSigRep1	Thymus 8w S	bigWig 1.000000 103179.000000	Thymus 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	60	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel Thymus 8w S\
subGroups view=Signal age=ADULT8WKS cellType=THYMUS strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfThymusC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 103179.000000\

wgEncodeSydhTfbsCh12CjunIggrabPk	CH12 c-Jun	narrowPeak	CH12 c-Jun TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	61	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 c-Jun TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks\
shortLabel CH12 c-Jun\
subGroups view=Peaks factor=cJUN cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12CjunIggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep2	Cortex - 2	bigWig 1.000000 1082007.000000	Cortex A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	61	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Cortex - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=CORTEX rep=rep2\
track wgEncodeCshlLongRnaSeqCortexAdult8wksMinusRawRep2\
type bigWig 1.000000 1082007.000000\

wgEncodeLicrHistoneEsb4H3k4me3ME0C57bl6StdSig	ES-Bruce4 H3K4m3	bigWig 0.120000 46.810001	ES-Bruce4 E0 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	61	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 E0 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-Bruce4 H3K4m3\
subGroups view=Signal age=E0 factor=H3K04ME3 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k4me3ME0C57bl6StdSig\
type bigWig 0.120000 46.810001\
viewLimits 0.2:10\

wgEncodeUwDnaseEscj7S129ME0HotspotsRep1	ES-CJ7 H 1	broadPeak	ES-CJ7 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	61	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-CJ7 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots\
shortLabel ES-CJ7 H 1\
subGroups view=Hotspots age=E0 cellType=ESCJ7 sex=M strain=a129S1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseEscj7S129ME0HotspotsRep1\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hPlusRawRep1	G1E-ER4 24hr P 1	bigWig 1.000000 3903140.000000	G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	61	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 24hr P 1\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=fDIFFD24H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hPlusRawRep1\
type bigWig 1.000000 3903140.000000\

wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep1	Heart 8w A 1	bam	Heart Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	61	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Heart 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=H2EART localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdSig	MEF 8w Pol2	bigWig 0.110000 40.720001	MEF Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	61	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel MEF 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMefPol2MAdult8wksC57bl6StdSig\
type bigWig 0.110000 40.720001\
viewLimits 0.2:3\

wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputSig	MEL Pol2	bigWig 1.000000 186.000000	MEL Pol2-4H8 TFBS ChIP-seq Signal from ENCODE/PSU	2	61	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Pol2-4H8 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel MEL Pol2\
subGroups view=Signal age=IMMORTAL factor=POL24H8 cellType=MEL control=INPUT treatment=aNONE rep=repP sex=M strain=C57BL6\
track wgEncodePsuTfbsMelPol24h8UImmortalC57bl6InputSig\
type bigWig 1.000000 186.000000\
viewLimits 5:50\

wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep1	Olfact 8wk Al 1	bam	Olfactory Bulb Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	61	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Olfactory Bulb Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Olfact 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=OLFACT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDgfTnaiveC57bl6MAdult8wksHotspotsRep1	T-Naive 8w H 1	broadPeak	T-Naive 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	61	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel T-Naive 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel T-Naive 8w H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=TNAIVE strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTnaiveC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeSydhTfbsCh12CjunIggrabSig	CH12 c-Jun	bigWig 1 57353	CH12 c-Jun TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	62	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 c-Jun TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig\
shortLabel CH12 c-Jun\
subGroups view=Signal factor=cJUN cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12CjunIggrabSig\
type bigWig 1 57353\

wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep2	Cortex + 2	bigWig 1.000000 2017463.000000	Cortex A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	62	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Cortex A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Cortex + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=CORTEX rep=rep2\
track wgEncodeCshlLongRnaSeqCortexAdult8wksPlusRawRep2\
type bigWig 1.000000 2017463.000000\

wgEncodeLicrHistoneEsb4H3k09acME0C57bl6StdPk	ES-Bruce4 H3K9a	broadPeak	ES-Bruce4 E0 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	62	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 E0 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-Bruce4 H3K9a\
subGroups view=Peaks age=E0 factor=H3K09AC cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k09acME0C57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseEscj7S129ME0PkRep1	ES-CJ7 P 1	narrowPeak	ES-CJ7 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	62	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-CJ7 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks\
shortLabel ES-CJ7 P 1\
subGroups view=Peaks age=E0 cellType=ESCJ7 sex=M strain=a129S1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseEscj7S129ME0PkRep1\
type narrowPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hMinusRawRep1	G1E-ER4 24hr M 1	bigWig -5729287.000000 -1.000000	G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	62	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 24hr M 1\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=fDIFFD24H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hMinusRawRep1\
type bigWig -5729287.000000 -1.000000\

wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep2	Heart 8w A 2	bam	Heart Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW	0	62	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Heart 8w A 2\
subGroups view=Alignments age=ADULT8WKS cellType=H2EART localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdPk	MEL Immort CTCF	broadPeak	MEL Immortal cells CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	62	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Immortal cells CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks\
shortLabel MEL Immort CTCF\
subGroups view=Peaks age=IMMORTAL factor=CTCF cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdPk\
type broadPeak\

wgEncodePsuTfbsMelTal1UImmortalC57bl6InputPk	MEL TAL1	broadPeak	MEL TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU	3	62	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL TAL1 TFBS ChIP-seq Peaks from ENCODE/PSU\
parent wgEncodePsuTfbsViewPeaks off\
shortLabel MEL TAL1\
subGroups view=Peaks age=IMMORTAL factor=TAL1 cellType=MEL control=INPUT treatment=aNONE rep=repP sex=M strain=C57BL6\
track wgEncodePsuTfbsMelTal1UImmortalC57bl6InputPk\
type broadPeak\

wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep2	Olfact 8wk Al 2	bam	Olfactory Bulb Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	62	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Olfactory Bulb Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Olfact 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=OLFACT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep1	T-Naive 8w P 1	narrowPeak	T-Naive 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	62	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel T-Naive 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel T-Naive 8w P 1\
subGroups view=Peaks age=ADULT8WKS cellType=TNAIVE strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeSydhTfbsCh12CmycIggrabPk	CH12 c-Myc	narrowPeak	CH12 c-Myc TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	63	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel CH12 c-Myc TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel CH12 c-Myc\
subGroups view=Peaks factor=cMYC cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12CmycIggrabPk\
type narrowPeak\

wgEncodeCshlLongRnaSeqCortexAdult8wksContigs	Cortex C	bed 6 +	Cortex A8 Long RNA-seq Contigs from ENCODE/CSHL	3	63	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Cortex C\
subGroups view=Contigs age=ADULT8WKS cellType=CORTEX rep=repP\
track wgEncodeCshlLongRnaSeqCortexAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneEsb4H3k09acME0C57bl6StdSig	ES-Bruce4 H3K9a	bigWig 0.150000 36.810001	ES-Bruce4 E0 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	63	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 E0 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-Bruce4 H3K9a\
subGroups view=Signal age=E0 factor=H3K09AC cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k09acME0C57bl6StdSig\
type bigWig 0.150000 36.810001\
viewLimits 0.2:5\

wgEncodeUwDnaseEscj7S129ME0SigRep1	ES-CJ7 S 1	bigWig 1.000000 74881.000000	ES-CJ7 DNaseI HS Signal Rep 1 from ENCODE/UW	2	63	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-CJ7 DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal\
shortLabel ES-CJ7 S 1\
subGroups view=Signal age=E0 cellType=ESCJ7 sex=M strain=a129S1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseEscj7S129ME0SigRep1\
type bigWig 1.000000 74881.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hAlnRep1	G1E-ER4 24hr A 1	bam	G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU	0	63	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 24hr A 1\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=fDIFFD24H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hAlnRep1\
type bam\

wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep1	Heart 8w MR 1	bigWig 1.000000 334960.000000	Heart Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	63	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel Heart 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=H2EART localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 334960.000000\

wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdSig	MEL Immort CTCF	bigWig 0.150000 142.000000	MEL Immortal cells CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	63	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal cells CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal\
shortLabel MEL Immort CTCF\
subGroups view=Signal age=IMMORTAL factor=CTCF cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMelCtcfMImmortalC57bl6StdSig\
type bigWig 0.150000 142.000000\
viewLimits 0.2:5\

wgEncodePsuTfbsMelTal1UImmortalC57bl6InputSig	MEL TAL1	bigWig 1.000000 346.000000	MEL TAL1 TFBS ChIP-seq Signal from ENCODE/PSU	2	63	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL TAL1 TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel MEL TAL1\
subGroups view=Signal age=IMMORTAL factor=TAL1 cellType=MEL control=INPUT treatment=aNONE rep=repP sex=M strain=C57BL6\
track wgEncodePsuTfbsMelTal1UImmortalC57bl6InputSig\
type bigWig 1.000000 346.000000\
viewLimits 2:300\

wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep1	OFlact 8wk Sg 1	bigWig 0.000000 46465.000000	Olfactory Bulb Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	63	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Olfactory Bulb Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel OFlact 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=OLFACT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep1\
type bigWig 0.000000 46465.000000\

wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep1	T-Naive 8w R 1	bigWig 1.000000 712972.000000	T-Naive 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	63	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel T-Naive 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel T-Naive 8w R 1\
subGroups view=RawSignal age=ADULT8WKS cellType=TNAIVE strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 712972.000000\

wgEncodeSydhTfbsCh12CmycIggrabSig	CH12 c-Myc	bigWig 1 56356	CH12 c-Myc TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	64	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel CH12 c-Myc TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel CH12 c-Myc\
subGroups view=Signal factor=cMYC cellType=CH12 control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsCh12CmycIggrabSig\
type bigWig 1 56356\

wgEncodeCshlLongRnaSeqCortexAdult8wksJunctions	Cortex J	bed 6 +	Cortex A8 Long RNA-seq Junctions from ENCODE/CSHL	0	64	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Cortex A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Cortex J\
subGroups view=SJunctions age=ADULT8WKS cellType=CORTEX rep=repP\
track wgEncodeCshlLongRnaSeqCortexAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneEsb4H3k09me3ME0C57bl6StdPk	ES-Bruce4 H3K9m3	broadPeak	ES-Bruce4 E0 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	64	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 E0 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-Bruce4 H3K9m3\
subGroups view=Peaks age=E0 factor=H3K09ME3 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k09me3ME0C57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseEscj7S129ME0HotspotsRep2	ES-CJ7 H 2	broadPeak	ES-CJ7 DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	64	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-CJ7 DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel ES-CJ7 H 2\
subGroups view=Hotspots age=E0 cellType=ESCJ7 sex=M strain=a129S1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseEscj7S129ME0HotspotsRep2\
type broadPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hPlusRawRep2	G1E-ER4 24hr P 2	bigWig 1.000000 1174207.000000	G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	64	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 24hr P 2\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=fDIFFD24H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hPlusRawRep2\
type bigWig 1.000000 1174207.000000\

wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep2	Heart 8w MR 2	bigWig 1.000000 530077.000000	Heart Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	64	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel Heart 8w MR 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=H2EART localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6MinusRawRep2\
type bigWig 1.000000 530077.000000\

wgEncodeLicrTfbsMelInputMImmortalC57bl6StdSig	MEL Immort Input	bigWig 0.150000 92.559998	MEL Immortal cells Input TFBS ChIP-seq Signal from ENCODE/LICR	2	64	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal cells Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel MEL Immort Input\
subGroups view=Signal age=IMMORTAL factor=INPUT cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMelInputMImmortalC57bl6StdSig\
type bigWig 0.150000 92.559998\

wgEncodePsuTfbsMelInputUImmortalC57bl6InputSig	MEL Input	bigWig 1.000000 132.000000	MEL Input TFBS ChIP-seq Signal from ENCODE/PSU	2	64	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Input TFBS ChIP-seq Signal from ENCODE/PSU\
parent wgEncodePsuTfbsViewSignal off\
shortLabel MEL Input\
subGroups view=Signal age=IMMORTAL factor=zINPUT cellType=MEL control=INPUT treatment=aNONE rep=repP sex=M strain=C57BL6\
track wgEncodePsuTfbsMelInputUImmortalC57bl6InputSig\
type bigWig 1.000000 132.000000\

wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep2	OFlact 8wk Sg 2	bigWig 0.000000 56111.000000	Olfactory Bulb Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	64	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Olfactory Bulb Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel OFlact 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=OLFACT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqOlfactCellPapMAdult8wksC57bl6SigRep2\
type bigWig 0.000000 56111.000000\

wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep1	T-Naive 8w S 1	bigWig 1.000000 147010.000000	T-Naive 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	64	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel T-Naive 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel T-Naive 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=TNAIVE strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 147010.000000\

wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep1V2	Duodenum Aln 1	bam	Duodenum A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	65	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Duodenum A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Duodenum Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=DUOD rep=rep1\
track wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep1V2\
type bam\

wgEncodeLicrHistoneEsb4H3k09me3ME0C57bl6StdSig	ES-Bruce4 H3K9m3	bigWig 0.110000 59.360001	ES-Bruce4 E0 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	65	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 E0 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-Bruce4 H3K9m3\
subGroups view=Signal age=E0 factor=H3K09ME3 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k09me3ME0C57bl6StdSig\
type bigWig 0.110000 59.360001\
viewLimits 0.2:2\

wgEncodeUwDnaseEscj7S129ME0PkRep2	ES-CJ7 P 2	narrowPeak	ES-CJ7 DNaseI HS Peaks Rep 2 from ENCODE/UW	3	65	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-CJ7 DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel ES-CJ7 P 2\
subGroups view=Peaks age=E0 cellType=ESCJ7 sex=M strain=a129S1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseEscj7S129ME0PkRep2\
type narrowPeak\

wgEncodeSydhTfbsEse14Hcfc1nb10068209StdPk	ES-E14 HCFC1 P	narrowPeak	ES-E14 HCFC1 (NB100-68209) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	65	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 HCFC1 (NB100-68209) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel ES-E14 HCFC1 P\
subGroups view=Peaks factor=HCFC1NB10068209 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhTfbsEse14Hcfc1nb10068209StdPk\
type narrowPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hMinusRawRep2	G1E-ER4 24hr M 2	bigWig -2109241.000000 -1.000000	G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	65	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 24hr M 2\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=fDIFFD24H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hMinusRawRep2\
type bigWig -2109241.000000 -1.000000\

wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep1	Heart 8w PR 1	bigWig 1.000000 334329.000000	Heart Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	65	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel Heart 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=H2EART localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 334329.000000\

wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdPk	MEL Immort Pol2	broadPeak	MEL Immortal cells Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	65	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Immortal cells Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks\
shortLabel MEL Immort Pol2\
subGroups view=Peaks age=IMMORTAL factor=POL2 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep1	Placenta 8wk Al 1	bam	Placenta Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	65	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Placenta Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Placenta 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=PLAC localization=CELL rnaExtract=PAP sex=F strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDgfTnaiveC57bl6MAdult8wksHotspotsRep2	T-Naive 8w H 2	broadPeak	T-Naive 8w C57BL/6 DNaseI DGF Hotspots Rep 2 from ENCODE/UW	0	65	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel T-Naive 8w C57BL/6 DNaseI DGF Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel T-Naive 8w H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=TNAIVE strain=C57BL6 treatment=NONE rep=rep2\
track wgEncodeUwDgfTnaiveC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep1	Duodenum - 1	bigWig 1.000000 663503.000000	Duodenum A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	66	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Duodenum A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Duodenum - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=DUOD rep=rep1\
track wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep1\
type bigWig 1.000000 663503.000000\

wgEncodeLicrHistoneEsb4H3k27acME0C57bl6StdPk	ES-Bruce4 H3K27a	broadPeak	ES-Bruce4 E0 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	66	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 E0 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-Bruce4 H3K27a\
subGroups view=Peaks age=E0 factor=H3K27AC cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k27acME0C57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseEscj7S129ME0SigRep2	ES-CJ7 S 2	bigWig 1.000000 85510.000000	ES-CJ7 DNaseI HS Signal Rep 2 from ENCODE/UW	2	66	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-CJ7 DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel ES-CJ7 S 2\
subGroups view=Signal age=E0 cellType=ESCJ7 sex=M strain=a129S1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseEscj7S129ME0SigRep2\
type bigWig 1.000000 85510.000000\

wgEncodeSydhTfbsEse14Hcfc1nb10068209StdSig	ES-E14 HCFC1 S	bigWig 1.000000 83707.000000	ES-E14 HCFC1 (NB100-68209) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	66	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 HCFC1 (NB100-68209) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel ES-E14 HCFC1 S\
subGroups view=Signal factor=HCFC1NB10068209 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhTfbsEse14Hcfc1nb10068209StdSig\
type bigWig 1.000000 83707.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hAlnRep2	G1E-ER4 24hr A 2	bam	G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU	0	66	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 24 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 24hr A 2\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=fDIFFD24H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd24hAlnRep2\
type bam\

wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep2	Heart 8w PR 2	bigWig 1.000000 528486.000000	Heart Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	66	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel Heart 8w PR 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=H2EART localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6PlusRawRep2\
type bigWig 1.000000 528486.000000\

wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdSig	MEL Immort Pol2	bigWig 0.120000 70.449997	MEL Immortal cells Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	66	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal cells Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal\
shortLabel MEL Immort Pol2\
subGroups view=Signal age=IMMORTAL factor=POL2 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsMelPol2MImmortalC57bl6StdSig\
type bigWig 0.120000 70.449997\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep2	Placenta 8wk Al 2	bam	Placenta Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	66	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Placenta Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Placenta 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=PLAC localization=CELL rnaExtract=PAP sex=F strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep2	T-Naive 8w P 2	narrowPeak	T-Naive 8w C57BL/6 DNaseI DGF Peaks Rep 2 from ENCODE/UW	0	66	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel T-Naive 8w C57BL/6 DNaseI DGF Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel T-Naive 8w P 2\
subGroups view=Peaks age=ADULT8WKS cellType=TNAIVE strain=C57BL6 treatment=NONE rep=rep2\
track wgEncodeUwDgfTnaiveC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep1	Duodenum + 1	bigWig 1.000000 1962905.000000	Duodenum A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	67	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Duodenum A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Duodenum + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=DUOD rep=rep1\
track wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep1\
type bigWig 1.000000 1962905.000000\

wgEncodeLicrHistoneEsb4H3k27acME0C57bl6StdSig	ES-Bruce4 H3K27a	bigWig 0.140000 42.669998	ES-Bruce4 E0 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	67	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 E0 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-Bruce4 H3K27a\
subGroups view=Signal age=E0 factor=H3K27AC cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k27acME0C57bl6StdSig\
type bigWig 0.140000 42.669998\
viewLimits 0.2:5\

wgEncodeUwDnaseEse14129olaME0HotspotsRep1	ES-E14 H 1	broadPeak	ES-E14 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	67	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel ES-E14 H 1\
subGroups view=Hotspots age=E0 cellType=ESE14 sex=M strain=a129OLA treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEse14129olaME0HotspotsRep1\
type broadPeak\

wgEncodeSydhTfbsEse14MafkStdPk	ES-E14 MafK_a	narrowPeak	ES-E14 MafK (ab50322) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	67	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 MafK (ab50322) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel ES-E14 MafK_a\
subGroups view=Peaks factor=MAFKAB50322 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhTfbsEse14MafkStdPk\
type narrowPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hPlusRawRep1	G1E-ER4 30hr P 1	bigWig 1.000000 4327197.000000	G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	67	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 30hr P 1\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=gDIFFD30H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hPlusRawRep1\
type bigWig 1.000000 4327197.000000\

wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep1	Heart 8w S 1	bigWig 1.000000 334960.000000	Heart Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	67	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel Heart 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=H2EART localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 334960.000000\

wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdPk	Olfact 8w CTCF	broadPeak	Olfactory Bulb Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	67	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Olfactory Bulb Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Olfact 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep1	Placenta 8wk Sg 1	bigWig 0.000000 65494.000000	Placenta Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	67	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Placenta 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=PLAC localization=CELL rnaExtract=PAP sex=F strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep1\
type bigWig 0.000000 65494.000000\

wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep2	T-Naive 8w R 2	bigWig 1.000000 607383.000000	T-Naive 8w C57BL/6 DNaseI DGF Raw Signal Rep 2 from ENCODE/UW	0	67	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel T-Naive 8w C57BL/6 DNaseI DGF Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel T-Naive 8w R 2\
subGroups view=RawSignal age=ADULT8WKS cellType=TNAIVE strain=C57BL6 treatment=NONE rep=rep2\
track wgEncodeUwDgfTnaiveC57bl6MAdult8wksRawRep2\
type bigWig 1.000000 607383.000000\

wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep2V2	Duodenum Aln 2	bam	Duodenum A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	68	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Duodenum A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Duodenum Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=DUOD rep=rep2\
track wgEncodeCshlLongRnaSeqDuodAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistoneEsb4H3k27me3ME0C57bl6StdPk	ES-Bruce4 H3K27m3	broadPeak	ES-Bruce4 E0 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	68	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 E0 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-Bruce4 H3K27m3\
subGroups view=Peaks age=E0 factor=H3K27ME3 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k27me3ME0C57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsEse14MafkStdSig	ES-E14 MafK_a	bigWig 1.000000 91890.000000	ES-E14 MafK (ab50322) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	68	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 MafK (ab50322) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel ES-E14 MafK_a\
subGroups view=Signal factor=MAFKAB50322 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhTfbsEse14MafkStdSig\
type bigWig 1.000000 91890.000000\

wgEncodeUwDnaseEse14129olaME0PkRep1	ES-E14 P 1	narrowPeak	ES-E14 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	68	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel ES-E14 P 1\
subGroups view=Peaks age=E0 cellType=ESE14 sex=M strain=a129OLA treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEse14129olaME0PkRep1\
type narrowPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hMinusRawRep1	G1E-ER4 30hr M 1	bigWig -7733400.000000 -1.000000	G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	68	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 30hr M 1\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=gDIFFD30H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hMinusRawRep1\
type bigWig -7733400.000000 -1.000000\

wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep2	Heart 8w S 2	bigWig 1.000000 530077.000000	Heart Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW	2	68	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel Heart 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=H2EART localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqHeartCellPolyaMAdult8wksC57bl6SigRep2\
type bigWig 1.000000 530077.000000\

wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdSig	Olfact 8w CTCF	bigWig 0.107427 50.025291	Olfactory Bulb Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	68	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Olfactory Bulb Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Olfact 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsOlfactCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.107427 50.025291\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep2	Placenta 8wk Sg 2	bigWig 0.000000 65494.000000	Placenta Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	68	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Placenta 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=PLAC localization=CELL rnaExtract=PAP sex=F strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqPlacCellPapFAdult8wksC57bl6SigRep2\
type bigWig 0.000000 65494.000000\

wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep2	T-Naive 8w S 2	bigWig 1.000000 111160.000000	T-Naive 8w C57BL/6 DNaseI DGF Signal Rep 2 from ENCODE/UW	2	68	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel T-Naive 8w C57BL/6 DNaseI DGF Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel T-Naive 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=TNAIVE strain=C57BL6 treatment=NONE rep=rep2\
track wgEncodeUwDgfTnaiveC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 111160.000000\

wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep2	Duodenum - 2	bigWig 1.000000 1258908.000000	Duodenum A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	69	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Duodenum A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Duodenum - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=DUOD rep=rep2\
track wgEncodeCshlLongRnaSeqDuodAdult8wksMinusRawRep2\
type bigWig 1.000000 1258908.000000\

wgEncodeLicrHistoneEsb4H3k27me3ME0C57bl6StdSig	ES-Bruce4 H3K27m3	bigWig 0.140000 30.559999	ES-Bruce4 E0 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	69	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 E0 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-Bruce4 H3K27m3\
subGroups view=Signal age=E0 factor=H3K27ME3 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k27me3ME0C57bl6StdSig\
type bigWig 0.140000 30.559999\
viewLimits 0.2:2\

wgEncodeUwDnaseEse14129olaME0SigRep1	ES-E14 S 1	bigWig 1.000000 192503.000000	ES-E14 DNaseI HS Signal Rep 1 from ENCODE/UW	2	69	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel ES-E14 S 1\
subGroups view=Signal age=E0 cellType=ESE14 sex=M strain=a129OLA treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEse14129olaME0SigRep1\
type bigWig 1.000000 192503.000000\

wgEncodeSydhTfbsEse14Zc3h11anb10074650StdPk	ES-E14 ZC3H11A P	narrowPeak	ES-E14 ZC3H11A (NB100-74650) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	69	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 ZC3H11A (NB100-74650) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel ES-E14 ZC3H11A P\
subGroups view=Peaks factor=ZC3H11ANB10074650 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhTfbsEse14Zc3h11anb10074650StdPk\
type narrowPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hAlnRep1	G1E-ER4 30hr A 1	bam	G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU	0	69	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 30hr A 1\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=gDIFFD30H rep=rep1\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hAlnRep1\
type bam\

wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6AlnRep1	Kidney 8w A 1	bam	Kidney Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	69	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Kidney 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=KIDNEY localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeLicrTfbsOlfactInputMAdult8wksC57bl6StdSig	Olfact 8w Input	bigWig 0.102227 41.708450	Olfactory Bulb Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	69	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Olfactory Bulb Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Olfact 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsOlfactInputMAdult8wksC57bl6StdSig\
type bigWig 0.102227 41.708450\

wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep1	SmInt 8wk Al 1	bam	Small Intestine Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	69	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel SmInt 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=SMINT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDgfTregC57bl6MAdult8wksHotspotsRep1	TReg 8w H	broadPeak	TReg 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	69	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel TReg 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel TReg 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=TREG strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTregC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep2	Duodenum + 2	bigWig 1.000000 2658856.000000	Duodenum A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	70	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Duodenum A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Duodenum + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=DUOD rep=rep2\
track wgEncodeCshlLongRnaSeqDuodAdult8wksPlusRawRep2\
type bigWig 1.000000 2658856.000000\

wgEncodeLicrHistoneEsb4H3k36me3ME0C57bl6StdPk	ES-Bruce4 H3K36m3	broadPeak	ES-Bruce4 E0 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	70	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-Bruce4 E0 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-Bruce4 H3K36m3\
subGroups view=Peaks age=E0 factor=H3K36ME3 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k36me3ME0C57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseEse14129olaME0HotspotsRep2	ES-E14 H 2	broadPeak	ES-E14 DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	70	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel ES-E14 H 2\
subGroups view=Hotspots age=E0 cellType=ESE14 sex=M strain=a129OLA treatment=zNONE rep=rep2\
track wgEncodeUwDnaseEse14129olaME0HotspotsRep2\
type broadPeak\

wgEncodeSydhTfbsEse14Zc3h11anb10074650StdSig	ES-E14 ZC3H11A S	bigWig 1.000000 105695.000000	ES-E14 ZC3H11A (NB100-74650) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	70	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 ZC3H11A (NB100-74650) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel ES-E14 ZC3H11A S\
subGroups view=Signal factor=ZC3H11ANB10074650 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhTfbsEse14Zc3h11anb10074650StdSig\
type bigWig 1.000000 105695.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hPlusRawRep2	G1E-ER4 30hr P 2	bigWig 1.000000 3705780.000000	G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	70	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel G1E-ER4 30hr P 2\
subGroups view=PlusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=gDIFFD30H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hPlusRawRep2\
type bigWig 1.000000 3705780.000000\

wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6MinusRawRep1	Kidney 8w MR 1	bigWig 1.000000 107185.000000	Kidney Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	70	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Kidney 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=KIDNEY localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 107185.000000\

wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdPk	Olfact 8w Pol2	broadPeak	Olfactory Bulb Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	70	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Olfactory Bulb Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Olfact 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep2	SmInt 8wk Al 2	bam	Small Intestine Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	70	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel SmInt 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=SMINT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDgfTregC57bl6MAdult8wksPkRep1	TReg 8w P	narrowPeak	TReg 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	70	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel TReg 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel TReg 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=TREG strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTregC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqDuodAdult8wksContigs	Duodenum C	bed 6 +	Duodenum A8 Long RNA-seq Contigs from ENCODE/CSHL	3	71	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Duodenum A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Duodenum C\
subGroups view=Contigs age=ADULT8WKS cellType=DUOD rep=repP\
track wgEncodeCshlLongRnaSeqDuodAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneEsb4H3k36me3ME0C57bl6StdSig	ES-Bruce4 H3K36m3	bigWig 0.140000 16.830000	ES-Bruce4 E0 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	71	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 E0 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-Bruce4 H3K36m3\
subGroups view=Signal age=E0 factor=H3K36ME3 cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4H3k36me3ME0C57bl6StdSig\
type bigWig 0.140000 16.830000\
viewLimits 0.2:2\

wgEncodeUwDnaseEse14129olaME0PkRep2	ES-E14 P 2	narrowPeak	ES-E14 DNaseI HS Peaks Rep 2 from ENCODE/UW	3	71	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel ES-E14 P 2\
subGroups view=Peaks age=E0 cellType=ESE14 sex=M strain=a129OLA treatment=zNONE rep=rep2\
track wgEncodeUwDnaseEse14129olaME0PkRep2\
type narrowPeak\

wgEncodeSydhTfbsEse14Znf384hpa004051StdPk	ES-E14 ZNF384 P	narrowPeak	ES-E14 ZNF384 (HPA004051) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	71	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 ZNF384 (HPA004051) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel ES-E14 ZNF384 P\
subGroups view=Peaks factor=ZNF384HPA004051 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhTfbsEse14Znf384hpa004051StdPk\
type narrowPeak\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hMinusRawRep2	G1E-ER4 30hr M 2	bigWig -4813498.000000 -1.000000	G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	71	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel G1E-ER4 30hr M 2\
subGroups view=MinusRawSignal age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=gDIFFD30H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hMinusRawRep2\
type bigWig -4813498.000000 -1.000000\

wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6PlusRawRep1	Kidney 8w PR 1	bigWig 1.000000 108237.000000	Kidney Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	71	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Kidney 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=KIDNEY localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 108237.000000\

wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdSig	Olfact 8w Pol2	bigWig 0.128951 53.643612	Olfactory Bulb Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	71	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Olfactory Bulb Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Olfact 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsOlfactPol2MAdult8wksC57bl6StdSig\
type bigWig 0.128951 53.643612\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep1	SmInt 8wk Sg 1	bigWig 0.000000 61922.000000	Small Intestine Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	71	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel SmInt 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=SMINT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep1\
type bigWig 0.000000 61922.000000\

wgEncodeUwDgfTregC57bl6MAdult8wksRawRep1	TReg 8w R	bigWig 1.000000 384314.000000	TReg 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	71	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel TReg 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel TReg 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=TREG strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTregC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 384314.000000\

wgEncodeCshlLongRnaSeqDuodAdult8wksJunctions	Duodenum J	bed 6 +	Duodenum A8 Long RNA-seq Junctions from ENCODE/CSHL	0	72	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Duodenum A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Duodenum J\
subGroups view=SJunctions age=ADULT8WKS cellType=DUOD rep=repP\
track wgEncodeCshlLongRnaSeqDuodAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneEsb4InputME0C57bl6StdSig	ES-Bruce4 Input	bigWig 0.130000 64.720001	ES-Bruce4 E0 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	72	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-Bruce4 E0 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-Bruce4 Input\
subGroups view=Signal age=E0 factor=INPUT cellType=ESB4 control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneEsb4InputME0C57bl6StdSig\
type bigWig 0.130000 64.720001\
viewLimits 0.2:5\

wgEncodeUwDnaseEse14129olaME0SigRep2	ES-E14 S 2	bigWig 1.000000 124940.000000	ES-E14 DNaseI HS Signal Rep 2 from ENCODE/UW	2	72	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel ES-E14 S 2\
subGroups view=Signal age=E0 cellType=ESE14 sex=M strain=a129OLA treatment=zNONE rep=rep2\
track wgEncodeUwDnaseEse14129olaME0SigRep2\
type bigWig 1.000000 124940.000000\

wgEncodeSydhTfbsEse14Znf384hpa004051StdSig	ES-E14 ZNF384 S	bigWig 1.000000 64093.000000	ES-E14 ZNF384 (HPA004051) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	72	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 ZNF384 (HPA004051) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel ES-E14 ZNF384 S\
subGroups view=Signal factor=ZNF384HPA004051 cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhTfbsEse14Znf384hpa004051StdSig\
type bigWig 1.000000 64093.000000\

wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hAlnRep2	G1E-ER4 30hr A 2	bam	G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU	0	72	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel G1E-ER4 Estradiol 30 hr 2x99D TC RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel G1E-ER4 30hr A 2\
subGroups view=Alignments age=E0 cellType=G1EER4T readType=R2X99D sex=M strain=s129 treatment=gDIFFD30H rep=rep2\
track wgEncodePsuRnaSeqG1eer4ME0S129R2x99dDiffd30hAlnRep2\
type bam\

wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6SigRep1	Kidney 8w S 1	bigWig 1.000000 108242.000000	Kidney Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	72	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Kidney 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=KIDNEY localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqKidneyCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 108242.000000\

wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdPk	SmInt 8w CTCF	broadPeak	Small Intestine Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	72	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel SmInt 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep2	SmInt 8wk Sg 2	bigWig 0.000000 65519.000000	Small Intestine Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	72	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel SmInt 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=SMINT localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqSmintCellPapMAdult8wksC57bl6SigRep2\
type bigWig 0.000000 65519.000000\

wgEncodeUwDgfTregC57bl6MAdult8wksSigRep1	TReg 8w S	bigWig 1.000000 62472.000000	TReg 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	72	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel TReg 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel TReg 8w S\
subGroups view=Signal age=ADULT8WKS cellType=TREG strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTregC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 62472.000000\

wgEncodeLicrHistoneEse14H3k04me1ME0129olaStdPk	ES-E14 H3K4m1	broadPeak	ES-E14 E0 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	73	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 E0 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-E14 H3K4m1\
subGroups view=Peaks age=E0 factor=H3K04ME1 cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k04me1ME0129olaStdPk\
type broadPeak\

wgEncodeSydhTfbsEse14InputStdSig	ES-E14 Input	bigWig 1.000000 255463.000000	ES-E14 Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	73	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel ES-E14 Input\
subGroups view=Signal factor=ZZZInputstd cellType=ESE14 control=STD treatment=zNONE\
track wgEncodeSydhTfbsEse14InputStdSig\
type bigWig 1.000000 255463.000000\

wgEncodeUwDnaseEsww6UknME0HotspotsRep1	ES-WW6 H 1	broadPeak	ES-WW6 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	73	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-WW6 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel ES-WW6 H 1\
subGroups view=Hotspots age=E0 cellType=ESWW6 sex=M strain=UKN treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEsww6UknME0HotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep1	FrontalLobe Aln 1	bam	Frontal Lobe A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	73	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Frontal Lobe A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel FrontalLobe Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=FLOBE rep=rep1\
track wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep1\
type bam\

wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep1	LgInt 8w A 1	bam	Large Intestine Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	73	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel LgInt 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=LGINT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep1	Megakaryocyte P 1	bigWig 1.000000 2187658.000000	Megakaryocyte 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	73	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal\
shortLabel Megakaryocyte P 1\
subGroups view=PlusRawSignal age=E14HALF cellType=MEGAKARYO readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep1\
type bigWig 1.000000 2187658.000000\

wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdSig	SmInt 8w CTCF	bigWig 0.130000 56.570000	Small Intestine Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	73	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel SmInt 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSmintCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.130000 56.570000\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep1	Spleen 8wk Al 1	bam	Spleen Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	73	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Spleen 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=SPLEEN localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDgfTregaC57bl6MAdult8wksHotspotsRep1	TReg-Act 8w H	broadPeak	TReg-Activated 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	73	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel TReg-Activated 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel TReg-Act 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=TREGA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTregaC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneEse14H3k04me1ME0129olaStdSig	ES-E14 H3K4m1	bigWig 0.130000 33.009998	ES-E14 E0 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	74	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 E0 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-E14 H3K4m1\
subGroups view=Signal age=E0 factor=H3K04ME1 cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k04me1ME0129olaStdSig\
type bigWig 0.130000 33.009998\
viewLimits 0.2:3\

wgEncodeUwDnaseEsww6UknME0PkRep1	ES-WW6 P 1	narrowPeak	ES-WW6 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	74	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-WW6 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel ES-WW6 P 1\
subGroups view=Peaks age=E0 cellType=ESWW6 sex=M strain=UKN treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEsww6UknME0PkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep1	FrontalLobe - 1	bigWig 1.000000 1155431.000000	Frontal Lobe A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	74	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Frontal Lobe A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel FrontalLobe - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=FLOBE rep=rep1\
track wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep1\
type bigWig 1.000000 1155431.000000\

wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep2	LgInt 8w A 2	bam	Large Intestine Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW	0	74	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel LgInt 8w A 2\
subGroups view=Alignments age=ADULT8WKS cellType=LGINT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep1	Megakaryocyte M 1	bigWig -4032882.000000 -1.000000	Megakaryocyte 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	74	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal\
shortLabel Megakaryocyte M 1\
subGroups view=MinusRawSignal age=E14HALF cellType=MEGAKARYO readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep1\
type bigWig -4032882.000000 -1.000000\

wgEncodeSydhTfbsMelBhlhe40cIggrabPk	MEL BHLHE40 P	narrowPeak	MEL BHLHE40 (NB100-1800) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	74	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL BHLHE40 (NB100-1800) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL BHLHE40 P\
subGroups view=Peaks factor=BHLHE40c cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelBhlhe40cIggrabPk\
type narrowPeak\

wgEncodeLicrTfbsSmintInputMAdult8wksC57bl6StdSig	SmInt 8w Input	bigWig 0.110000 33.189999	Small Intestine Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	74	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel SmInt 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSmintInputMAdult8wksC57bl6StdSig\
type bigWig 0.110000 33.189999\

wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep2	Spleen 8wk Al 2	bam	Spleen Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	74	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Spleen 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=SPLEEN localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDgfTregaC57bl6MAdult8wksPkRep1	TReg-Act 8w P	narrowPeak	TReg-Activated 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	74	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel TReg-Activated 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel TReg-Act 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=TREGA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTregaC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeLicrHistoneEse14H3k04me3ME0129olaStdPk	ES-E14 H3K4m3	broadPeak	ES-E14 E0 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	75	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 E0 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-E14 H3K4m3\
subGroups view=Peaks age=E0 factor=H3K04ME3 cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k04me3ME0129olaStdPk\
type broadPeak\

wgEncodeUwDnaseEsww6UknME0SigRep1	ES-WW6 S 1	bigWig 1.000000 82908.000000	ES-WW6 DNaseI HS Signal Rep 1 from ENCODE/UW	2	75	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-WW6 DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel ES-WW6 S 1\
subGroups view=Signal age=E0 cellType=ESWW6 sex=M strain=UKN treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEsww6UknME0SigRep1\
type bigWig 1.000000 82908.000000\

wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep1	FrontalLobe + 1	bigWig 1.000000 1301024.000000	Frontal Lobe A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	75	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Frontal Lobe A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel FrontalLobe + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=FLOBE rep=rep1\
track wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep1\
type bigWig 1.000000 1301024.000000\

wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep1	LgInt 8w MR 1	bigWig 1.000000 180585.000000	Large Intestine Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	75	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel LgInt 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LGINT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 180585.000000\

wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep1	Megakaryocyte A 1	bam	Megakaryocyte 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU	0	75	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryocyte 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel Megakaryocyte A 1\
subGroups view=Alignments age=E14HALF cellType=MEGAKARYO readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep1\
type bam\

wgEncodeSydhTfbsMelBhlhe40cIggrabSig	MEL BHLHE40 S	bigWig 1.000000 111235.000000	MEL BHLHE40 (NB100-1800) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	75	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL BHLHE40 (NB100-1800) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL BHLHE40 S\
subGroups view=Signal factor=BHLHE40c cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelBhlhe40cIggrabSig\
type bigWig 1.000000 111235.000000\

wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdPk	SI 8w Pol2	broadPeak	Small Intestine Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	75	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel SI 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep1	Spleen 8wk Sg 1	bigWig 4.000000 65511.000000	Spleen Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	75	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Spleen 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=SPLEEN localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep1\
type bigWig 4.000000 65511.000000\

wgEncodeUwDgfTregaC57bl6MAdult8wksRawRep1	TReg-Act 8w R	bigWig 1.000000 1174126.000000	TReg-Activated 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	75	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel TReg-Activated 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel TReg-Act 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=TREGA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTregaC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 1174126.000000\

wgEncodeLicrHistoneEse14H3k04me3ME0129olaStdSig	ES-E14 H3K4m3	bigWig 0.110000 65.769997	ES-E14 E0 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	76	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 E0 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-E14 H3K4m3\
subGroups view=Signal age=E0 factor=H3K04ME3 cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k04me3ME0129olaStdSig\
type bigWig 0.110000 65.769997\
viewLimits 0.2:10\

wgEncodeUwDnaseEsww6UknME0HotspotsRep2	ES-WW6 H 2	broadPeak	ES-WW6 DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	76	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-WW6 DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel ES-WW6 H 2\
subGroups view=Hotspots age=E0 cellType=ESWW6 sex=M strain=UKN treatment=zNONE rep=rep2\
track wgEncodeUwDnaseEsww6UknME0HotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep2	FrontalLobe Aln 2	bam	Frontal Lobe A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	76	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Frontal Lobe A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel FrontalLobe Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=FLOBE rep=rep2\
track wgEncodeCshlLongRnaSeqFlobeAdult8wksAlnRep2\
type bam\

wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep2	LgInt 8w MR 2	bigWig 1.000000 416478.000000	Large Intestine Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	76	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel LgInt 8w MR 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LGINT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6MinusRawRep2\
type bigWig 1.000000 416478.000000\

wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep2	Megakaryocyte P 2	bigWig 1.000000 301191.000000	Megakaryocyte 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	76	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel Megakaryocyte P 2\
subGroups view=PlusRawSignal age=E14HALF cellType=MEGAKARYO readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dPlusRawRep2\
type bigWig 1.000000 301191.000000\
viewLimits 1:3000\

wgEncodeSydhTfbsMelChd1nb10060411IggrabPk	MEL CHD1 P	narrowPeak	MEL CHD1 (NB100-60411) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	76	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL CHD1 (NB100-60411) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL CHD1 P\
subGroups view=Peaks factor=CHD1NB10060411 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelChd1nb10060411IggrabPk\
type narrowPeak\

wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdSig	SmInt 8w Pol2	bigWig 0.120000 35.160000	Small Intestine Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	76	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel SmInt 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSmintPol2MAdult8wksC57bl6StdSig\
type bigWig 0.120000 35.160000\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep2	Spleen 8wk Sg 2	bigWig 4.000000 65521.000000	Spleen Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	76	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Spleen 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=SPLEEN localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqSpleenCellPapMAdult8wksC57bl6SigRep2\
type bigWig 4.000000 65521.000000\

wgEncodeUwDgfTregaC57bl6MAdult8wksSigRep1	TReg-Act 8w S	bigWig 1.000000 270816.000000	TReg-Activated 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	76	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel TReg-Activated 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel TReg-Act 8w S\
subGroups view=Signal age=ADULT8WKS cellType=TREGA strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfTregaC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 270816.000000\

wgEncodeUwDgfWbrainC57bl6MAdult8wksHotspotsRep1	Brain 8w H	broadPeak	Brain 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	77	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Brain 8w C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots\
shortLabel Brain 8w H\
subGroups view=Hotspots age=ADULT8WKS cellType=WBRAIN strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfWbrainC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneEse14H3k09acME0129olaStdPk	ES-E14 H3K9a	broadPeak	ES-E14 E0 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	77	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 E0 H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-E14 H3K9a\
subGroups view=Peaks age=E0 factor=H3K09AC cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k09acME0129olaStdPk\
type broadPeak\

wgEncodeUwDnaseEsww6UknME0PkRep2	ES-WW6 P 2	narrowPeak	ES-WW6 DNaseI HS Peaks Rep 2 from ENCODE/UW	3	77	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-WW6 DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel ES-WW6 P 2\
subGroups view=Peaks age=E0 cellType=ESWW6 sex=M strain=UKN treatment=zNONE rep=rep2\
track wgEncodeUwDnaseEsww6UknME0PkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep2	FrontalLobe - 2	bigWig 1.000000 998833.000000	Frontal Lobe A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	77	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Frontal Lobe A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel FrontalLobe - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=FLOBE rep=rep2\
track wgEncodeCshlLongRnaSeqFlobeAdult8wksMinusRawRep2\
type bigWig 1.000000 998833.000000\

wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep1	LgInt 8w PR 1	bigWig 1.000000 180503.000000	Large Intestine Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	77	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel LgInt 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LGINT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 180503.000000\

wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep2	Megakaryocyte M 2	bigWig -278887.000000 -1.000000	Megakaryocyte  2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	77	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Megakaryocyte  2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel Megakaryocyte M 2\
subGroups view=MinusRawSignal age=E14HALF cellType=MEGAKARYO readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dMinusRawRep2\
type bigWig -278887.000000 -1.000000\
viewLimits -3000:-1\

wgEncodeSydhTfbsMelChd1nb10060411IggrabSig	MEL CHD1 S	bigWig 1.000000 74165.000000	MEL CHD1 (NB100-60411) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	77	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL CHD1 (NB100-60411) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL CHD1 S\
subGroups view=Signal factor=CHD1NB10060411 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelChd1nb10060411IggrabSig\
type bigWig 1.000000 74165.000000\

wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdPk	Spleen 8w CTCF	broadPeak	Spleen Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	77	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Spleen 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep1	Testis 8wk Al 1	bam	Testis Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	77	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Testis 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=TESTIS localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDgfWbrainC57bl6MAdult8wksPkRep1	Brain 8w P	narrowPeak	Brain 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	78	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Brain 8w C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks\
shortLabel Brain 8w P\
subGroups view=Peaks age=ADULT8WKS cellType=WBRAIN strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfWbrainC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeLicrHistoneEse14H3k09acME0129olaStdSig	ES-E14 H3K9a	bigWig 0.150000 39.680000	ES-E14 E0 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	78	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 E0 H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-E14 H3K9a\
subGroups view=Signal age=E0 factor=H3K09AC cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k09acME0129olaStdSig\
type bigWig 0.150000 39.680000\
viewLimits 0.2:5\

wgEncodeUwDnaseEsww6UknME0SigRep2	ES-WW6 S 2	bigWig 1.000000 90027.000000	ES-WW6 DNaseI HS Signal Rep 2 from ENCODE/UW	2	78	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-WW6 DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel ES-WW6 S 2\
subGroups view=Signal age=E0 cellType=ESWW6 sex=M strain=UKN treatment=zNONE rep=rep2\
track wgEncodeUwDnaseEsww6UknME0SigRep2\
type bigWig 1.000000 90027.000000\

wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep2	FrontalLobe + 2	bigWig 1.000000 1178288.000000	Frontal Lobe A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	78	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Frontal Lobe A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel FrontalLobe + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=FLOBE rep=rep2\
track wgEncodeCshlLongRnaSeqFlobeAdult8wksPlusRawRep2\
type bigWig 1.000000 1178288.000000\

wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep2	LgInt 8w PR 2	bigWig 1.000000 295554.000000	Large Intestine Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	78	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel LgInt 8w PR 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LGINT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6PlusRawRep2\
type bigWig 1.000000 295554.000000\

wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep2	Megakaryocyte A 2	bam	Megakaryocyte 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU	0	78	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Megakaryocyte 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel Megakaryocyte A 2\
subGroups view=Alignments age=E14HALF cellType=MEGAKARYO readType=R2X99D sex=B strain=CD1 treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqMegakaryoBE14halfCd1R2x99dAlnRep2\
type bam\

wgEncodeSydhTfbsMelChd2ab68301IggrabPk	MEL CHD2	narrowPeak	MEL CHD2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	78	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL CHD2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL CHD2\
subGroups view=Peaks factor=CHD2AB68301 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelChd2ab68301IggrabPk\
type narrowPeak\

wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdSig	Spleen 8w CTCF	bigWig 0.200000 53.349998	Spleen Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	78	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Spleen 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSpleenCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.200000 53.349998\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep2	Testis 8wk Al 2	bam	Testis Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	78	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Testis 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=TESTIS localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDgfWbrainC57bl6MAdult8wksRawRep1	Brain 8w R	bigWig 1.000000 191994.000000	Brain 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	79	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Brain 8w C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal\
shortLabel Brain 8w R\
subGroups view=RawSignal age=ADULT8WKS cellType=WBRAIN strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfWbrainC57bl6MAdult8wksRawRep1\
type bigWig 1.000000 191994.000000\

wgEncodeLicrHistoneEse14H3k27acME0129olaStdPk	ES-E14 H3K27a	broadPeak	ES-E14 E0 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	79	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 E0 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-E14 H3K27a\
subGroups view=Peaks age=E0 factor=H3K27AC cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k27acME0129olaStdPk\
type broadPeak\

wgEncodeUwDnaseEsww6koUknME0HotspotsRep1	ES-WW6 F1KO H 1	broadPeak	ES-WW6 F1KO DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	79	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-WW6 F1KO DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel ES-WW6 F1KO H 1\
subGroups view=Hotspots age=E0 cellType=ESWW6KO sex=M strain=UKN treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEsww6koUknME0HotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqFlobeAdult8wksContigs	FrontalLobe  C	bed 6 +	Frontal Lobe A8 Long RNA-seq Contigs from ENCODE/CSHL	3	79	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Frontal Lobe A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel FrontalLobe  C\
subGroups view=Contigs age=ADULT8WKS cellType=FLOBE rep=repP\
track wgEncodeCshlLongRnaSeqFlobeAdult8wksContigs\
type bed 6 +\

wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep1	LgInt 8w S 1	bigWig 1.000000 180585.000000	Large Intestine Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	79	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel LgInt 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=LGINT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 180585.000000\

wgEncodeSydhTfbsMelChd2ab68301IggrabSig	MEL CHD2	bigWig 1.000000 121731.000000	MEL CHD2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	79	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL CHD2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL CHD2\
subGroups view=Signal factor=CHD2AB68301 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelChd2ab68301IggrabSig\
type bigWig 1.000000 121731.000000\

wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep1	MEL S 1	bigWig 1.000000 308139.000000	MEL 1x45 RNA-seq Signal Rep 1 from ENCODE/PSU	2	79	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL 1x45 RNA-seq Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal\
shortLabel MEL S 1\
subGroups view=Signal age=IMMORTAL cellType=MEL readType=R1X45 sex=M strain=UKN treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep1\
type bigWig 1.000000 308139.000000\

wgEncodeLicrTfbsSpleenInputMAdult8wksC57bl6StdSig	Spleen 8w Input	bigWig 0.130000 31.219999	Spleen Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	79	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Spleen 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSpleenInputMAdult8wksC57bl6StdSig\
type bigWig 0.130000 31.219999\

wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep1	Testis 8wk Sg 1	bigWig 0.000000 28146.000000	Testis Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	79	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Testis 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=TESTIS localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep1\
type bigWig 0.000000 28146.000000\

wgEncodeUwDgfWbrainC57bl6MAdult8wksSigRep1	Brain 8w S	bigWig 1.000000 44749.000000	Brain 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	80	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Brain 8w C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal\
shortLabel Brain 8w S\
subGroups view=Signal age=ADULT8WKS cellType=WBRAIN strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfWbrainC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 44749.000000\

wgEncodeLicrHistoneEse14H3k27acME0129olaStdSig	ES-E14 H3K27a	bigWig 0.140000 38.610001	ES-E14 E0 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	80	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 E0 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-E14 H3K27a\
subGroups view=Signal age=E0 factor=H3K27AC cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k27acME0129olaStdSig\
type bigWig 0.140000 38.610001\
viewLimits 0.2:5\

wgEncodeUwDnaseEsww6koUknME0PkRep1	ES-WW6 F1KO P 1	narrowPeak	ES-WW6 F1KO DNaseI HS Peaks Rep 1 from ENCODE/UW	3	80	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-WW6 F1KO DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel ES-WW6 F1KO P 1\
subGroups view=Peaks age=E0 cellType=ESWW6KO sex=M strain=UKN treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEsww6koUknME0PkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqFlobeAdult8wksJunctions	FrontalLobe J	bed 6 +	Frontal Lobe A8 Long RNA-seq Junctions from ENCODE/CSHL	0	80	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Frontal Lobe A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel FrontalLobe J\
subGroups view=SJunctions age=ADULT8WKS cellType=FLOBE rep=repP\
track wgEncodeCshlLongRnaSeqFlobeAdult8wksJunctions\
type bed 6 +\

wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep2	LgInt 8w S 2	bigWig 1.000000 416478.000000	Large Intestine Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW	2	80	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel LgInt 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=LGINT localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqLgintCellPolyaMAdult8wksC57bl6SigRep2\
type bigWig 1.000000 416478.000000\

wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep1	MEL A 1	bam	MEL 1x45 RNA-seq Alignments Rep 1 from ENCODE/PSU	0	80	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL 1x45 RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel MEL A 1\
subGroups view=Alignments age=IMMORTAL cellType=MEL readType=R1X45 sex=M strain=UKN treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep1\
type bam\

wgEncodeSydhTfbsMelCorestsc30189IggrabPk	MEL COREST P	narrowPeak	MEL COREST (sc-30189) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	80	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL COREST (sc-30189) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL COREST P\
subGroups view=Peaks factor=CORESTSC30189 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelCorestsc30189IggrabPk\
type narrowPeak\

wgEncodeLicrTfbsSpleenPol2MAdult8wksC57bl6StdPk	Spleen 8w Pol2	broadPeak	Spleen Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	80	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Spleen 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSpleenPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep2	Testis 8wk Sg 2	bigWig 0.000000 31418.000000	Testis Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	80	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Testis 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=TESTIS localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqTestisCellPapMAdult8wksC57bl6SigRep2\
type bigWig 0.000000 31418.000000\

wgEncodeUwDgfWbrainC57bl6ME14halfHotspotsRep1	Brain E14.5 H	broadPeak	Brain E14.5 C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	81	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Brain E14.5 C57BL/6 DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots\
shortLabel Brain E14.5 H\
subGroups view=Hotspots age=E14HALF cellType=WBRAIN strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfWbrainC57bl6ME14halfHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneEse14H3k36me3ME0129olaStdPk	ES-E14 H3K36m3	broadPeak	ES-E14 E0 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	81	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-E14 E0 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel ES-E14 H3K36m3\
subGroups view=Peaks age=E0 factor=H3K36ME3 cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k36me3ME0129olaStdPk\
type broadPeak\

wgEncodeUwDnaseEsww6koUknME0SigRep1	ES-WW6 F1KO S 1	bigWig 1.000000 51340.000000	ES-WW6 F1KO DNaseI HS Signal Rep 1 from ENCODE/UW	2	81	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-WW6 F1KO DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel ES-WW6 F1KO S 1\
subGroups view=Signal age=E0 cellType=ESWW6KO sex=M strain=UKN treatment=zNONE rep=rep1\
track wgEncodeUwDnaseEsww6koUknME0SigRep1\
type bigWig 1.000000 51340.000000\

wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep1V2	GenFatPad Aln 1	bam	Genital Fat Pad A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	81	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Genital Fat Pad A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel GenFatPad Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=GFAT rep=rep1\
track wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep1V2\
type bam\

wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep1	Lv S_C 8w A 1	bam	Liver C57BL6 Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	81	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver C57BL6 Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Lv S_C 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeSydhTfbsMelCorestsc30189IggrabSig	MEL COREST S	bigWig 1.000000 86280.000000	MEL COREST (sc-30189) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	81	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL COREST (sc-30189) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL COREST S\
subGroups view=Signal factor=CORESTSC30189 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelCorestsc30189IggrabSig\
type bigWig 1.000000 86280.000000\

wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep2	MEL S 2	bigWig 1.000000 424496.000000	MEL 1x45 RNA-seq Signal Rep 2 from ENCODE/PSU	2	81	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL 1x45 RNA-seq Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal off\
shortLabel MEL S 2\
subGroups view=Signal age=IMMORTAL cellType=MEL readType=R1X45 sex=M strain=UKN treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqMelMImmortalUknR1x45SigRep2\
type bigWig 1.000000 424496.000000\

wgEncodeLicrTfbsSpleenPol2MAdult8wksC57bl6StdSig	Spleen 8w Pol2	bigWig 0.130000 26.709999	Spleen Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	81	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Spleen 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsSpleenPol2MAdult8wksC57bl6StdSig\
type bigWig 0.130000 26.709999\
viewLimits 0.2:3\

wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep1	Thymus 8wk Al 1	bam	Thymus Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR	0	81	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Thymus 8wk Al 1\
subGroups view=Alignments age=ADULT8WKS cellType=THYMUS localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDgfWbrainC57bl6ME14halfPkRep1	Brain E14.5 P	narrowPeak	Brain E14.5 C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	82	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Brain E14.5 C57BL/6 DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks\
shortLabel Brain E14.5 P\
subGroups view=Peaks age=E14HALF cellType=WBRAIN strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfWbrainC57bl6ME14halfPkRep1\
type narrowPeak\

wgEncodeLicrHistoneEse14H3k36me3ME0129olaStdSig	ES-E14 H3K36m3	bigWig 0.110000 39.830002	ES-E14 E0 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	82	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-E14 E0 H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel ES-E14 H3K36m3\
subGroups view=Signal age=E0 factor=H3K36ME3 cellType=ESE14 control=STD sex=M strain=A129Ola\
track wgEncodeLicrHistoneEse14H3k36me3ME0129olaStdSig\
type bigWig 0.110000 39.830002\
viewLimits 0.2:2\

wgEncodeUwDnaseEsww6koUknME0HotspotsRep2	ES-WW6 F1KO H 2	broadPeak	ES-WW6 F1KO DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	82	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-WW6 F1KO DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel ES-WW6 F1KO H 2\
subGroups view=Hotspots age=E0 cellType=ESWW6KO sex=M strain=UKN treatment=zNONE rep=rep2\
track wgEncodeUwDnaseEsww6koUknME0HotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep1	GenFatPad - 1	bigWig 1.000000 390244.000000	Genital Fat Pad A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	82	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Genital Fat Pad A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel GenFatPad - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=GFAT rep=rep1\
track wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep1\
type bigWig 1.000000 390244.000000\

wgEncodeUwRnaSeqLiverCellPolyaME14halfS129AlnRep1	Lv S_1 E14.5 A 1	bam	Liver 129 Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/UW	0	82	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 129 Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Lv S_1 E14.5 A 1\
subGroups view=Alignments age=E14HALF cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=A1S129 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaME14halfS129AlnRep1\
type bam\

wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep2	MEL A 2	bam	MEL 1x45 RNA-seq Alignments Rep 2 from ENCODE/PSU	0	82	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL 1x45 RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel MEL A 2\
subGroups view=Alignments age=IMMORTAL cellType=MEL readType=R1X45 sex=M strain=UKN treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqMelMImmortalUknR1x45AlnRep2\
type bam\

wgEncodeSydhTfbsMelCtcfbDm2p5dStdPk	MEL CTCF_S	narrowPeak	MEL CTCF (SC-15914) DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	82	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL CTCF (SC-15914) DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL CTCF_S\
subGroups view=Peaks factor=CTCFb cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhTfbsMelCtcfbDm2p5dStdPk\
type narrowPeak\

wgEncodeLicrTfbsTestisCtcfMAdult8wksC57bl6StdPk	Testis 8w CTCF	broadPeak	Testis Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	82	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Testis 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsTestisCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep2	Thymus 8wk Al 2	bam	Thymus Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR	0	82	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Thymus 8wk Al 2\
subGroups view=Alignments age=ADULT8WKS cellType=THYMUS localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDgfWbrainC57bl6ME14halfRawRep1	Brain E14.5 R	bigWig 1.000000 288905.000000	Brain E14.5 C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	83	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Brain E14.5 C57BL/6 DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal\
shortLabel Brain E14.5 R\
subGroups view=RawSignal age=E14HALF cellType=WBRAIN strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfWbrainC57bl6ME14halfRawRep1\
type bigWig 1.000000 288905.000000\

wgEncodeUwDnaseEsww6koUknME0PkRep2	ES-WW6 F1KO P 2	narrowPeak	ES-WW6 F1KO DNaseI HS Peaks Rep 2 from ENCODE/UW	3	83	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ES-WW6 F1KO DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel ES-WW6 F1KO P 2\
subGroups view=Peaks age=E0 cellType=ESWW6KO sex=M strain=UKN treatment=zNONE rep=rep2\
track wgEncodeUwDnaseEsww6koUknME0PkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep1	GenFatPad + 1	bigWig 1.000000 753772.000000	Genital Fat Pad A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	83	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Genital Fat Pad A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel GenFatPad + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=GFAT rep=rep1\
track wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep1\
type bigWig 1.000000 753772.000000\

wgEncodeLicrHistoneHeartH3k4me1MAdult8wksC57bl6StdPk	Heart 8w H3K4m1	broadPeak	Heart 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	83	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 8w H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k4me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6AlnRep1	Lv S_C E14.5 A 1	bam	Liver C57BL6 Embryonic day 14.5 RNA-seq Alignments Rep 1 ENCODE/UW	0	83	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver C57BL6 Embryonic day 14.5 RNA-seq Alignments Rep 1 ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Lv S_C E14.5 A 1\
subGroups view=Alignments age=E14HALF cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6AlnRep1\
type bam\

wgEncodeSydhTfbsMelCtcfbDm2p5dStdSig	MEL CTCF_S D	bigWig 1.000000 49927.000000	MEL CTCF (SC-15914) DMSO 2% ChIP-seq TFBS Signal from ENCODE/Stanford/Yale	2	83	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL CTCF (SC-15914) DMSO 2% ChIP-seq TFBS Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL CTCF_S D\
subGroups view=Signal factor=CTCFb cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhTfbsMelCtcfbDm2p5dStdSig\
type bigWig 1.000000 49927.000000\

wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep1	MEL DMSO 2% S 1	bigWig 1.000000 1357689.000000	MEL DMSO 2.0pct 1x45 RNA-seq Signal Rep 1 from ENCODE/PSU	2	83	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL DMSO 2.0pct 1x45 RNA-seq Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal\
shortLabel MEL DMSO 2% S 1\
subGroups view=Signal age=IMMORTAL cellType=MEL readType=R1X45 sex=M strain=UKN treatment=bDM2P5D rep=rep1\
track wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep1\
type bigWig 1.000000 1357689.000000\

wgEncodeLicrTfbsTestisCtcfMAdult8wksC57bl6StdSig	Testis 8w CTCF	bigWig 0.120000 51.270000	Testis Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	83	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Testis 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsTestisCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.120000 51.270000\
viewLimits 0.2:5\

wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep1	Thymus 8wk Sg 1	bigWig 0.000000 65184.000000	Thymus Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR	2	83	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Thymus 8wk Sg 1\
subGroups view=Signal age=ADULT8WKS cellType=THYMUS localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep1\
type bigWig 0.000000 65184.000000\

wgEncodeUwDgfWbrainC57bl6ME14halfSigRep1	Brain E14.5 S	bigWig 1.000000 63709.000000	Brain E14.5 C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW	2	84	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Brain E14.5 C57BL/6 DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal\
shortLabel Brain E14.5 S\
subGroups view=Signal age=E14HALF cellType=WBRAIN strain=C57BL6 treatment=NONE rep=rep1\
track wgEncodeUwDgfWbrainC57bl6ME14halfSigRep1\
type bigWig 1.000000 63709.000000\

wgEncodeUwDnaseEsww6koUknME0SigRep2	ES-WW6 F1KO S 2	bigWig 1.000000 58605.000000	ES-WW6 F1KO DNaseI HS Signal Rep 2 from ENCODE/UW	2	84	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ES-WW6 F1KO DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel ES-WW6 F1KO S 2\
subGroups view=Signal age=E0 cellType=ESWW6KO sex=M strain=UKN treatment=zNONE rep=rep2\
track wgEncodeUwDnaseEsww6koUknME0SigRep2\
type bigWig 1.000000 58605.000000\

wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep2V2	GenFatPad Aln 2	bam	Genital Fat Pad A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	84	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Genital Fat Pad A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel GenFatPad Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=GFAT rep=rep2\
track wgEncodeCshlLongRnaSeqGfatAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistoneHeartH3k04me1UE14halfC57bl6StdPk	Heart 14.5 H3K4m1	broadPeak	Heart E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	84	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 14.5 H3K4m1\
subGroups view=Peaks age=E14HALF factor=H3K04ME1 cellType=HEART control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k04me1UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep2	Lv S_C 8w A 2	bam	Liver C57BL6 Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW	0	84	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver C57BL6 Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Lv S_C 8w A 2\
subGroups view=Alignments age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeSydhTfbsMelCtcfbIggrabPk	MEL CTCF	narrowPeak	MEL CTCF TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	84	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL CTCF TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks\
shortLabel MEL CTCF\
subGroups view=Peaks factor=CTCFb cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelCtcfbIggrabPk\
type narrowPeak\

wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep1	MEL DMSO 2% A 1	bam	MEL DMSO 2.0pct 1x45 RNA-seq Alignments Rep 1 from ENCODE/PSU	0	84	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL DMSO 2.0pct 1x45 RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel MEL DMSO 2% A 1\
subGroups view=Alignments age=IMMORTAL cellType=MEL readType=R1X45 sex=M strain=UKN treatment=bDM2P5D rep=rep1\
track wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep1\
type bam\

wgEncodeLicrTfbsTestisInputMAdult8wksC57bl6StdSig	Testis 8w Input	bigWig 0.130000 59.860001	Testis Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	84	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Testis 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsTestisInputMAdult8wksC57bl6StdSig\
type bigWig 0.130000 59.860001\

wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep2	Thymus 8wk Sg 2	bigWig 0.000000 65415.000000	Thymus Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR	2	84	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal off\
shortLabel Thymus 8wk Sg 2\
subGroups view=Signal age=ADULT8WKS cellType=THYMUS localization=CELL rnaExtract=PAP sex=M strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqThymusCellPapMAdult8wksC57bl6SigRep2\
type bigWig 0.000000 65415.000000\

wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep1	Brain E14.5 Al 1	bam	Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR	0	85	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Brain E14.5 Al 1\
subGroups view=Alignments age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep1\
type bam\

wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep1	Fat Pad H 1	broadPeak	Fat Pad DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	85	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Fat Pad DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Fat Pad H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=FAT sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep2	GenFatPad - 2	bigWig 1.000000 278328.000000	Genital Fat Pad A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	85	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Genital Fat Pad A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel GenFatPad - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=GFAT rep=rep2\
track wgEncodeCshlLongRnaSeqGfatAdult8wksMinusRawRep2\
type bigWig 1.000000 278328.000000\

wgEncodeLicrHistoneHeartH3k4me1MAdult8wksC57bl6StdSig	Heart 8w H3K4m1	bigWig 0.130000 15.600000	Heart 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	85	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 8w H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k4me1MAdult8wksC57bl6StdSig\
type bigWig 0.130000 15.600000\
viewLimits 0.2:3\

wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep1	Lv S_C 8w MR 1	bigWig 1.000000 402549.000000	Liver C57BL6 Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	85	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL6 Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel Lv S_C 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 402549.000000\

wgEncodeSydhTfbsMelCtcfsc15914IggrabSig	MEL CTCF	bigWig 1.000000 62645.000000	MEL CTCF TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	85	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL CTCF TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig\
shortLabel MEL CTCF\
subGroups view=Signal factor=CTCFb cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelCtcfsc15914IggrabSig\
type bigWig 1.000000 62645.000000\

wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep2	MEL DMSO 2% S 2	bigWig 1.000000 758536.000000	MEL DMSO 2.0pct 1x45 RNA-seq Signal Rep 2 from ENCODE/PSU	2	85	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL DMSO 2.0pct 1x45 RNA-seq Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewSignal off\
shortLabel MEL DMSO 2% S 2\
subGroups view=Signal age=IMMORTAL cellType=MEL readType=R1X45 sex=M strain=UKN treatment=bDM2P5D rep=rep2\
track wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dSigRep2\
type bigWig 1.000000 758536.000000\

wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdPk	Testis 8w Pol2	broadPeak	Testis Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	85	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Testis 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDgfZhbtc4129olaME0Diffb24hHotspotsRep1	ZhBTc4 diff E0 H	broadPeak	ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	85	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel ZhBTc4 diff E0 H\
subGroups view=Hotspots age=E0 cellType=ZHBTC4 strain=A129OLA treatment=DIFFB24H rep=rep1\
track wgEncodeUwDgfZhbtc4129olaME0Diffb24hHotspotsRep1\
type broadPeak\

wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep2	Brain E14.5 Al 2	bam	Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR	0	86	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewAlignments off\
shortLabel Brain E14.5 Al 2\
subGroups view=Alignments age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6AlnRep2\
type bam\

wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep1	Fat Pad P 1	narrowPeak	Fat Pad DNaseI HS Peaks Rep 1 from ENCODE/UW	3	86	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Fat Pad DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Fat Pad P 1\
subGroups view=Peaks age=ADULT8WKS cellType=FAT sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep2	GenFatPad + 2	bigWig 1.000000 504194.000000	Genital Fat Pad A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	86	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Genital Fat Pad A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel GenFatPad + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=GFAT rep=rep2\
track wgEncodeCshlLongRnaSeqGfatAdult8wksPlusRawRep2\
type bigWig 1.000000 504194.000000\

wgEncodeLicrHistoneHeartH3k04me1UE14halfC57bl6StdSig	Heart 14.5 H3K4m1	bigWig 0.100000 18.980000	Heart E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	86	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 14.5 H3K4m1\
subGroups view=Signal age=E14HALF factor=H3K04ME1 cellType=HEART control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k04me1UE14halfC57bl6StdSig\
type bigWig 0.100000 18.980000\
viewLimits 0.2:3\

wgEncodeUwRnaSeqLiverCellPolyaME14halfS129MinusRawRep1	Lv S_1 E14.5 MR 1	bigWig 1.000000 653623.000000	Liver 129 Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	86	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 129 Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel Lv S_1 E14.5 MR 1\
subGroups view=MinusRawSignal age=E14HALF cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=A1S129 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaME14halfS129MinusRawRep1\
type bigWig 1.000000 653623.000000\

wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep2	MEL DMSO 2% A 2	bam	MEL DMSO 2.0pct 1x45 RNA-seq Alignments Rep 2 from ENCODE/PSU	0	86	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL DMSO 2.0pct 1x45 RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel MEL DMSO 2% A 2\
subGroups view=Alignments age=IMMORTAL cellType=MEL readType=R1X45 sex=M strain=UKN treatment=bDM2P5D rep=rep2\
track wgEncodePsuRnaSeqMelMImmortalUknR1x45Dm2p5dAlnRep2\
type bam\

wgEncodeSydhTfbsMelE2f4IggrabPk	MEL E2F4	narrowPeak	MEL E2F4 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	86	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL E2F4 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL E2F4\
subGroups view=Peaks factor=E2F4 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelE2f4IggrabPk\
type narrowPeak\

wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdSig	Testis 8w Pol2	bigWig 0.120000 43.590000	Testis Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	86	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Testis 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsTestisPol2MAdult8wksC57bl6StdSig\
type bigWig 0.120000 43.590000\
viewLimits 0.2:3\

wgEncodeUwDgfZhbtc4129olaME0Diffb24hPkRep1	ZhBTc4 diff E0 P	narrowPeak	ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	86	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel ZhBTc4 diff E0 P\
subGroups view=Peaks age=E0 cellType=ZHBTC4 strain=A129OLA treatment=DIFFB24H rep=rep1\
track wgEncodeUwDgfZhbtc4129olaME0Diffb24hPkRep1\
type narrowPeak\

wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep1	Brain E14.5 Sg 1	bigWig 0.000000 64995.000000	Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR	2	87	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel Brain E14.5 Sg 1\
subGroups view=Signal age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep1\
track wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep1\
type bigWig 0.000000 64995.000000\

wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep1	Fat Pad S 1	bigWig 1.000000 52562.000000	Fat Pad DNaseI HS Signal Rep 1 from ENCODE/UW	2	87	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Fat Pad DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Fat Pad S 1\
subGroups view=Signal age=ADULT8WKS cellType=FAT sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 52562.000000\

wgEncodeCshlLongRnaSeqGfatAdult8wksContigs	GenFatPad C	bed 6 +	Genital Fat Pad A8 Long RNA-seq Contigs from ENCODE/CSHL	3	87	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Genital Fat Pad A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs\
shortLabel GenFatPad C\
subGroups view=Contigs age=ADULT8WKS cellType=GFAT rep=repP\
track wgEncodeCshlLongRnaSeqGfatAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneHeartH3k4me3MAdult8wksC57bl6StdPk	Heart 8w H3K4m3	broadPeak	Heart 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	87	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 8w H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k4me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6MinusRawRep1	Lv S_C E14.5 MR 1	bigWig 1.000000 194747.000000	Liver C57BL6 Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	87	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL6 Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel Lv S_C E14.5 MR 1\
subGroups view=MinusRawSignal age=E14HALF cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6MinusRawRep1\
type bigWig 1.000000 194747.000000\

wgEncodeSydhTfbsMelE2f4IggrabSig	MEL E2F4	bigWig 1.000000 91713.000000	MEL E2F4 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	87	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL E2F4 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL E2F4\
subGroups view=Signal factor=E2F4 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelE2f4IggrabSig\
type bigWig 1.000000 91713.000000\

wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep1	MEP P 1	bigWig 1.000000 1133190.000000	MEP 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU	2	87	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEP 2x99D RNA-seq Plus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal\
shortLabel MEP P 1\
subGroups view=PlusRawSignal age=ADULT5WKS cellType=MEP readType=R2X99D sex=F strain=C57BL6J treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep1\
type bigWig 1.000000 1133190.000000\

wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdPk	Thymus 8w CTCF	broadPeak	Thymus Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	87	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus Adult 8 weeks CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Thymus 8w CTCF\
subGroups view=Peaks age=A1DULT8WKS factor=CTCF cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDgfZhbtc4129olaME0Diffb24hRawRep1	ZhBTc4 diff E0 R	bigWig 1.000000 759516.000000	ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Raw Signal Rep 1 ENCODE/UW	0	87	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Raw Signal Rep 1 ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel ZhBTc4 diff E0 R\
subGroups view=RawSignal age=E0 cellType=ZHBTC4 strain=A129OLA treatment=DIFFB24H rep=rep1\
track wgEncodeUwDgfZhbtc4129olaME0Diffb24hRawRep1\
type bigWig 1.000000 759516.000000\

wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep2	Brain E14.5 Sg 2	bigWig 0.000000 65459.000000	Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR	2	88	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/LICR\
parent wgEncodeLicrRnaSeqViewSignal\
shortLabel Brain E14.5 Sg 2\
subGroups view=Signal age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=PAP sex=U strain=C57BL6 rep=rep2\
track wgEncodeLicrRnaSeqWbrainCellPapUE14halfC57bl6SigRep2\
type bigWig 0.000000 65459.000000\

wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep2	Fat Pad H 2	broadPeak	Fat Pad DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	88	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Fat Pad DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Fat Pad H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=FAT sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseFatC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqGfatAdult8wksJunctions	GenFatPad J	bed 6 +	Genital Fat Pad A8 Long RNA-seq Junctions from ENCODE/CSHL	0	88	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Genital Fat Pad A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel GenFatPad J\
subGroups view=SJunctions age=ADULT8WKS cellType=GFAT rep=repP\
track wgEncodeCshlLongRnaSeqGfatAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneHeartH3k04me3UE14halfC57bl6StdPk	Heart 14.5 H3K4m3	broadPeak	Heart E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	88	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 14.5 H3K4m3\
subGroups view=Peaks age=E14HALF factor=H3K04ME3 cellType=HEART control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k04me3UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep2	Lv S_C 8w MR 2	bigWig 1.000000 155864.000000	Liver C57BL6 Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	88	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL6 Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel Lv S_C 8w MR 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6MinusRawRep2\
type bigWig 1.000000 155864.000000\

wgEncodeSydhTfbsMelEts1IggrabPk	MEL ETS1	narrowPeak	MEL ETS1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	88	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL ETS1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL ETS1\
subGroups view=Peaks factor=ETS1 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelEts1IggrabPk\
type narrowPeak\

wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep1	MEP M 1	bigWig -1321352.000000 -1.000000	MEP 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU	2	88	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEP 2x99D RNA-seq Minus Raw Signal Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal\
shortLabel MEP M 1\
subGroups view=MinusRawSignal age=ADULT5WKS cellType=MEP readType=R2X99D sex=F strain=C57BL6J treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep1\
type bigWig -1321352.000000 -1.000000\

wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdSig	Thymus 8w CTCF	bigWig 0.105497 132.820557	Thymus Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	88	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Thymus 8w CTCF\
subGroups view=Signal age=A1DULT8WKS factor=CTCF cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsThymusCtcfMAdult8wksC57bl6StdSig\
type bigWig 0.105497 132.820557\
viewLimits 0.2:5\

wgEncodeUwDgfZhbtc4129olaME0Diffb24hSigRep1	ZhBTc4 diff E0 S	bigWig 1.000000 130305.000000	ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Signal Rep 1 from ENCODE/UW	2	88	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ZhBTc4 E0 129/Ola differentiated 24 hr DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel ZhBTc4 diff E0 S\
subGroups view=Signal age=E0 cellType=ZHBTC4 strain=A129OLA treatment=DIFFB24H rep=rep1\
track wgEncodeUwDgfZhbtc4129olaME0Diffb24hSigRep1\
type bigWig 1.000000 130305.000000\

wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep2	Fat Pad P 2	narrowPeak	Fat Pad DNaseI HS Peaks Rep 2 from ENCODE/UW	3	89	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Fat Pad DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Fat Pad P 2\
subGroups view=Peaks age=ADULT8WKS cellType=FAT sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseFatC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeLicrHistoneHeartH3k4me3MAdult8wksC57bl6StdSig	Heart 8w H3K4m3	bigWig 0.130000 67.910004	Heart 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	89	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 8w H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k4me3MAdult8wksC57bl6StdSig\
type bigWig 0.130000 67.910004\
viewLimits 0.2:10\

wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep1V2	Heart Aln 1	bam	Heart A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	89	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Heart Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=HEART rep=rep1\
track wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep1V2\
type bam\

wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep1	Lv S_C 8w PR 1	bigWig 1.000000 287434.000000	Liver C57BL6 Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	89	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL6 Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel Lv S_C 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 287434.000000\

wgEncodeSydhTfbsMelEts1IggrabSig	MEL ETS1	bigWig 1.000000 37310.000000	MEL ETS1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	89	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL ETS1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL ETS1\
subGroups view=Signal factor=ETS1 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelEts1IggrabSig\
type bigWig 1.000000 37310.000000\

wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep1	MEP A 1	bam	MEP 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU	0	89	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEP 2x99D RNA-seq Alignments Rep 1 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel MEP A 1\
subGroups view=Alignments age=ADULT5WKS cellType=MEP readType=R2X99D sex=F strain=C57BL6J treatment=aNONE rep=rep1\
track wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep1\
type bam\

wgEncodeLicrTfbsThymusInputMAdult8wksC57bl6StdSig	Thymus 8w Input	bigWig 0.122860 69.354546	Thymus Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR	2	89	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Thymus 8w Input\
subGroups view=Signal age=A1DULT8WKS factor=INPUT cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsThymusInputMAdult8wksC57bl6StdSig\
type bigWig 0.122860 69.354546\

wgEncodeUwDgfZhbtc4129olaME0HotspotsRep1	ZhBTc4 E0 H	broadPeak	ZhBTc4 E0 129/Ola DNaseI DGF Hotspots Rep 1 from ENCODE/UW	0	89	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ZhBTc4 E0 129/Ola DNaseI DGF Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewHotspots off\
shortLabel ZhBTc4 E0 H\
subGroups view=Hotspots age=E0 cellType=ZHBTC4 strain=A129OLA treatment=NONE rep=rep1\
track wgEncodeUwDgfZhbtc4129olaME0HotspotsRep1\
type broadPeak\

wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep2	Fat Pad S 2	bigWig 1.000000 53274.000000	Fat Pad DNaseI HS Signal Rep 2 from ENCODE/UW	2	90	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Fat Pad DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Fat Pad S 2\
subGroups view=Signal age=ADULT8WKS cellType=FAT sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseFatC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 53274.000000\

wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep1	Heart - 1	bigWig 1.000000 2343090.000000	Heart A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	90	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel Heart - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=HEART rep=rep1\
track wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep1\
type bigWig 1.000000 2343090.000000\

wgEncodeLicrHistoneHeartH3k04me3UE14halfC57bl6StdSig	Heart 14.5 H3K4m3	bigWig 0.110000 72.550003	Heart E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	90	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 14.5 H3K4m3\
subGroups view=Signal age=E14HALF factor=H3K04ME3 cellType=HEART control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k04me3UE14halfC57bl6StdSig\
type bigWig 0.110000 72.550003\
viewLimits 0.2:10\

wgEncodeUwRnaSeqLiverCellPolyaME14halfS129PlusRawRep1	Lv S_1 E14.5 PR 1	bigWig 1.000000 742349.000000	Liver 129 Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	90	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 129 Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel Lv S_1 E14.5 PR 1\
subGroups view=PlusRawSignal age=E14HALF cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=A1S129 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaME14halfS129PlusRawRep1\
type bigWig 1.000000 742349.000000\

wgEncodeSydhTfbsMelGata1Dm2p5dStdPk	MEL GATA-1	narrowPeak	MEL GATA-1 DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	90	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL GATA-1 DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL GATA-1\
subGroups view=Peaks factor=GATA1SC265 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhTfbsMelGata1Dm2p5dStdPk\
type narrowPeak\

wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep2	MEP P 2	bigWig 1.000000 1251896.000000	MEP 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU	2	90	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEP 2x99D RNA-seq Plus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewPlusRawSignal off\
shortLabel MEP P 2\
subGroups view=PlusRawSignal age=ADULT5WKS cellType=MEP readType=R2X99D sex=F strain=C57BL6J treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dPlusRawRep2\
type bigWig 1.000000 1251896.000000\

wgEncodeLicrTfbsThymusPol2MAdult8wksC57bl6StdPk	Thymus 8w Pol2	broadPeak	Thymus Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	90	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus Adult 8 weeks Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Thymus 8w Pol2\
subGroups view=Peaks age=A1DULT8WKS factor=POL2 cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsThymusPol2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDgfZhbtc4129olaME0PkRep1	ZhBTc4 E0 P	narrowPeak	ZhBTc4 E0 129/Ola DNaseI DGF Peaks Rep 1 from ENCODE/UW	0	90	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel ZhBTc4 E0 129/Ola DNaseI DGF Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewPeaks off\
shortLabel ZhBTc4 E0 P\
subGroups view=Peaks age=E0 cellType=ZHBTC4 strain=A129OLA treatment=NONE rep=rep1\
track wgEncodeUwDgfZhbtc4129olaME0PkRep1\
type narrowPeak\

wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep1	Fibroblast H 1	broadPeak	Fibroblast DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	91	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Fibroblast DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Fibroblast H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=FIBROBLAST sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep1	Heart + 1	bigWig 1.000000 3000713.000000	Heart A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	91	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Heart + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=HEART rep=rep1\
track wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep1\
type bigWig 1.000000 3000713.000000\

wgEncodeLicrHistoneHeartH3k09acMAdult8wksC57bl6StdPk	Heart 8w H3K9a	broadPeak	Heart 8w H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	91	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart 8w H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 8w H3K9a\
subGroups view=Peaks age=A1DLT8W factor=H3K09AC cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k09acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6PlusRawRep1	Lv S_C E14.5 PR 1	bigWig 1.000000 164985.000000	Liver C57BL6 Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	91	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL6 Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel Lv S_C E14.5 PR 1\
subGroups view=PlusRawSignal age=E14HALF cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6PlusRawRep1\
type bigWig 1.000000 164985.000000\

wgEncodeSydhTfbsMelGata1Dm2p5dStdSig	MEL GATA-1 D	bigWig 1.000000 38707.000000	MEL GATA-1 DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	91	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL GATA-1 DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL GATA-1 D\
subGroups view=Signal factor=GATA1SC265 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhTfbsMelGata1Dm2p5dStdSig\
type bigWig 1.000000 38707.000000\

wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep2	MEP M 2	bigWig -2408713.000000 -1.000000	MEP 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU	2	91	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEP 2x99D RNA-seq Minus Raw Signal Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewMinusRawSignal off\
shortLabel MEP M 2\
subGroups view=MinusRawSignal age=ADULT5WKS cellType=MEP readType=R2X99D sex=F strain=C57BL6J treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dMinusRawRep2\
type bigWig -2408713.000000 -1.000000\

wgEncodeLicrTfbsThymusPol2MAdult8wksC57bl6StdSig	Thymus 8w Pol2	bigWig 0.191412 108.530518	Thymus Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	91	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Thymus 8w Pol2\
subGroups view=Signal age=A1DULT8WKS factor=POL2 cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrTfbsThymusPol2MAdult8wksC57bl6StdSig\
type bigWig 0.191412 108.530518\
viewLimits 0.2:3\

wgEncodeUwDgfZhbtc4129olaME0RawRep1	ZhBTc4 E0 R	bigWig 1.000000 563374.000000	ZhBTc4 E0 129/Ola DNaseI DGF Raw Signal Rep 1 from ENCODE/UW	0	91	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ZhBTc4 E0 129/Ola DNaseI DGF Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewRawSignal off\
shortLabel ZhBTc4 E0 R\
subGroups view=RawSignal age=E0 cellType=ZHBTC4 strain=A129OLA treatment=NONE rep=rep1\
track wgEncodeUwDgfZhbtc4129olaME0RawRep1\
type bigWig 1.000000 563374.000000\

wgEncodeLicrTfbsWbrainCtcfUE14halfC57bl6StdPk	Brain 14.5 CTCF	broadPeak	Whole Brain Embryonic day 14.5 CTCF TFBS ChIP-seq Peaks from ENCODE/LICR	3	92	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 CTCF TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Brain 14.5 CTCF\
subGroups view=Peaks age=E14HALF factor=CTCF cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsWbrainCtcfUE14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep1	Fibroblast P 1	narrowPeak	Fibroblast DNaseI HS Peaks Rep 1 from ENCODE/UW	3	92	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Fibroblast DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Fibroblast P 1\
subGroups view=Peaks age=ADULT8WKS cellType=FIBROBLAST sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeLicrHistoneHeartH3k09acMAdult8wksC57bl6StdSig	Heart 8w H3K9a	bigWig 0.130000 32.660000	Heart 8w H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	92	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 8w H3K9a\
subGroups view=Signal age=A1DLT8W factor=H3K09AC cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k09acMAdult8wksC57bl6StdSig\
type bigWig 0.130000 32.660000\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep2V2	Heart Aln 2	bam	Heart A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	92	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Heart Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=HEART rep=rep2\
track wgEncodeCshlLongRnaSeqHeartAdult8wksAlnRep2V2\
type bam\

wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep2	Lv S_C 8w PR 2	bigWig 1.000000 96877.000000	Liver C57BL6 Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	92	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL6 Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel Lv S_C 8w PR 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6PlusRawRep2\
type bigWig 1.000000 96877.000000\

wgEncodeSydhTfbsMelGata1IggratPk	MEL GATA-1	narrowPeak	MEL GATA-1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	92	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL GATA-1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks\
shortLabel MEL GATA-1\
subGroups view=Peaks factor=GATA1SC265 cellType=MEL control=IGGRAT treatment=zNONE\
track wgEncodeSydhTfbsMelGata1IggratPk\
type narrowPeak\

wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep2	MEP A 2	bam	MEP 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU	0	92	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEP 2x99D RNA-seq Alignments Rep 2 from ENCODE/PSU\
parent wgEncodePsuRnaSeqViewAlignments off\
shortLabel MEP A 2\
subGroups view=Alignments age=ADULT5WKS cellType=MEP readType=R2X99D sex=F strain=C57BL6J treatment=aNONE rep=rep2\
track wgEncodePsuRnaSeqMepFAdult5wksC57bl6jR2x99dAlnRep2\
type bam\

wgEncodeUwDgfZhbtc4129olaME0SigRep1	ZhBTc4 E0 S	bigWig 1.000000 90713.000000	ZhBTc4 E0 129/Ola DNaseI DGF Signal Rep 1 from ENCODE/UW	2	92	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ZhBTc4 E0 129/Ola DNaseI DGF Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDgfViewSignal off\
shortLabel ZhBTc4 E0 S\
subGroups view=Signal age=E0 cellType=ZHBTC4 strain=A129OLA treatment=NONE rep=rep1\
track wgEncodeUwDgfZhbtc4129olaME0SigRep1\
type bigWig 1.000000 90713.000000\

wgEncodeLicrTfbsWbrainCtcfUE14halfC57bl6StdSig	Brain 14.5 CTCF	bigWig 0.100000 57.000000	Whole Brain Embryonic day 14.5 CTCF TFBS ChIP-seq Signal from ENCODE/LICR	2	93	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 CTCF TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Brain 14.5 CTCF\
subGroups view=Signal age=E14HALF factor=CTCF cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsWbrainCtcfUE14halfC57bl6StdSig\
type bigWig 0.100000 57.000000\
viewLimits 0.2:5\

wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep1	Fibroblast S 1	bigWig 1.000000 76418.000000	Fibroblast DNaseI HS Signal Rep 1 from ENCODE/UW	2	93	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Fibroblast DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Fibroblast S 1\
subGroups view=Signal age=ADULT8WKS cellType=FIBROBLAST sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 76418.000000\

wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep2	Heart - 2	bigWig 1.000000 2232933.000000	Heart A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	93	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel Heart - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=HEART rep=rep2\
track wgEncodeCshlLongRnaSeqHeartAdult8wksMinusRawRep2\
type bigWig 1.000000 2232933.000000\

wgEncodeLicrHistoneHeartH3k27acMAdult8wksC57bl6StdPk	Heart 8w H3K27a	broadPeak	Heart 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	93	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 8w H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep1	Lv S_C 8w S 1	bigWig 1.000000 402550.000000	Liver C57BL6 Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	93	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL6 Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel Lv S_C 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 402550.000000\

wgEncodeSydhTfbsMelGata1IggratSig	MEL GATA-1	bigWig 1 56526	MEL GATA-1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	93	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL GATA-1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig\
shortLabel MEL GATA-1\
subGroups view=Signal factor=GATA1SC265 cellType=MEL control=IGGRAT treatment=zNONE\
track wgEncodeSydhTfbsMelGata1IggratSig\
type bigWig 1 56526\

wgEncodeLicrTfbsWbrainInputUE14halfC57bl6StdSig	Brain 14.5 Input	bigWig 0.130000 22.879999	Whole Brain Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR	2	94	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 Input TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Brain 14.5 Input\
subGroups view=Signal age=E14HALF factor=INPUT cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsWbrainInputUE14halfC57bl6StdSig\
type bigWig 0.130000 22.879999\

wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep2	Fibroblast H 2	broadPeak	Fibroblast DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	94	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Fibroblast DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Fibroblast H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=FIBROBLAST sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseFibroblastC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep2	Heart + 2	bigWig 1.000000 2947116.000000	Heart A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	94	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Heart + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=HEART rep=rep2\
track wgEncodeCshlLongRnaSeqHeartAdult8wksPlusRawRep2\
type bigWig 1.000000 2947116.000000\

wgEncodeLicrHistoneHeartH3k27acUE14halfC57bl6StdPk	Heart 14.5 H3K27a	broadPeak	Heart E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	94	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 14.5 H3K27a\
subGroups view=Peaks age=E14HALF factor=H3K27AC cellType=HEART control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k27acUE14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqLiverCellPolyaME14halfS129SigRep1	Lv S_1 E14.5 S 1	bigWig 1.000000 742349.000000	Liver 129 Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/UW	2	94	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 129 Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel Lv S_1 E14.5 S 1\
subGroups view=Signal age=E14HALF cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=A1S129 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaME14halfS129SigRep1\
type bigWig 1.000000 742349.000000\

wgEncodeSydhTfbsMelGcn5IggrabPk	MEL GCN5 P	narrowPeak	MEL GCN5 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	94	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL GCN5 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL GCN5 P\
subGroups view=Peaks factor=GCN5 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelGcn5IggrabPk\
type narrowPeak\

wgEncodeLicrTfbsWbrainPol2UE14halfC57bl6StdPk	Brain 14.5 Pol2	broadPeak	Whole Brain Embryonic day 14.5 Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR	3	95	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 Pol2 TFBS ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrTfbsViewPeaks off\
shortLabel Brain 14.5 Pol2\
subGroups view=Peaks age=E14HALF factor=POL2 cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsWbrainPol2UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep2	Fibroblast P 2	narrowPeak	Fibroblast DNaseI HS Peaks Rep 2 from ENCODE/UW	3	95	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Fibroblast DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Fibroblast P 2\
subGroups view=Peaks age=ADULT8WKS cellType=FIBROBLAST sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseFibroblastC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeLicrHistoneHeartH3k27acMAdult8wksC57bl6StdSig	Heart 8w H3K27a	bigWig 0.100000 33.759998	Heart 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	95	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 8w H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.100000 33.759998\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqHeartAdult8wksContigs	Heart C	bed 6 +	Heart A8 Long RNA-seq Contigs from ENCODE/CSHL	3	95	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs\
shortLabel Heart C\
subGroups view=Contigs age=ADULT8WKS cellType=HEART rep=repP\
track wgEncodeCshlLongRnaSeqHeartAdult8wksContigs\
type bed 6 +\

wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6SigRep1	Lv S_C E14.5 S 1	bigWig 1.000000 194747.000000	Liver C57BL6 Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/UW	2	95	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL6 Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel Lv S_C E14.5 S 1\
subGroups view=Signal age=E14HALF cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLiverCellPolyaME14halfC57bl6SigRep1\
type bigWig 1.000000 194747.000000\

wgEncodeSydhTfbsMelGcn5IggrabSig	MEL GCN5 S	bigWig 1.000000 496.000000	MEL GCN5 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	95	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL GCN5 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL GCN5 S\
subGroups view=Signal factor=GCN5 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelGcn5IggrabSig\
type bigWig 1.000000 496.000000\

wgEncodeLicrTfbsWbrainPol2UE14halfC57bl6StdSig	Brain 14.5 Pol2	bigWig 0.140000 80.190002	Whole Brain Embryonic day 14.5 Pol2 TFBS ChIP-seq Signal from ENCODE/LICR	2	96	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 Pol2 TFBS ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrTfbsViewSignal off\
shortLabel Brain 14.5 Pol2\
subGroups view=Signal age=E14HALF factor=POL2 cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrTfbsWbrainPol2UE14halfC57bl6StdSig\
type bigWig 0.140000 80.190002\
viewLimits 0.2:3\

wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep2	Fibroblast S 2	bigWig 1.000000 91985.000000	Fibroblast DNaseI HS Signal Rep 2 from ENCODE/UW	2	96	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Fibroblast DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Fibroblast S 2\
subGroups view=Signal age=ADULT8WKS cellType=FIBROBLAST sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseFibroblastC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 91985.000000\

wgEncodeLicrHistoneHeartH3k27acUE14halfC57bl6StdSig	Heart 14.5 H3K27a	bigWig 0.110000 38.139999	Heart E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	96	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 14.5 H3K27a\
subGroups view=Signal age=E14HALF factor=H3K27AC cellType=HEART control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k27acUE14halfC57bl6StdSig\
type bigWig 0.110000 38.139999\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqHeartAdult8wksJunctions	Heart J	bed 6 +	Heart A8 Long RNA-seq Junctions from ENCODE/CSHL	0	96	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Heart J\
subGroups view=SJunctions age=ADULT8WKS cellType=HEART rep=repP\
track wgEncodeCshlLongRnaSeqHeartAdult8wksJunctions\
type bed 6 +\

wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep2	Lv S_C 8w S 2	bigWig 1.000000 155866.000000	Liver C57BL6 Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW	2	96	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL6 Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel Lv S_C 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=LIVER localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqLiverCellPolyaMAdult8wksC57bl6SigRep2\
type bigWig 1.000000 155866.000000\

wgEncodeSydhTfbsMelHcfc1nb10068209IggrabPk	MEL HCFC1 P	narrowPeak	MEL HCFC1 (NB100-68209) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	96	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL HCFC1 (NB100-68209) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL HCFC1 P\
subGroups view=Peaks factor=HCFC1NB10068209 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelHcfc1nb10068209IggrabPk\
type narrowPeak\

wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep1	Fore Limb Bud H 1	broadPeak	Fore Limb Bud DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	97	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Fore Limb Bud DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Fore Limb Bud H 1\
subGroups view=Hotspots age=E11HALF cellType=FLBUD sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneHeartH3k27me3MAdult8wksC57bl6StdPk	Heart 8w H3K27m3	broadPeak	Heart 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	97	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 8w H3K27m3\
subGroups view=Peaks age=A1DLT8W factor=H3K27ME3 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k27me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep1V2	Kidney Aln 1	bam	Kidney A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	97	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Kidney Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=KIDNEY rep=rep1\
track wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep1V2\
type bam\

wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6AlnRep1	Lung 8w A 1	bam	Lung Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	97	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Lung 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=LUNG localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeSydhTfbsMelHcfc1nb10068209IggrabSig	MEL HCFC1 S	bigWig 1.000000 34023.000000	MEL HCFC1 (NB100-68209) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	97	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL HCFC1 (NB100-68209) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL HCFC1 S\
subGroups view=Signal factor=HCFC1NB10068209 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelHcfc1nb10068209IggrabSig\
type bigWig 1.000000 34023.000000\

wgEncodeUwDnaseFlbudCd1ME11halfPkRep1	Fore Limb Bud P 1	narrowPeak	Fore Limb Bud DNaseI HS Peaks Rep 1 from ENCODE/UW	3	98	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Fore Limb Bud DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Fore Limb Bud P 1\
subGroups view=Peaks age=E11HALF cellType=FLBUD sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseFlbudCd1ME11halfPkRep1\
type narrowPeak\

wgEncodeLicrHistoneHeartH3k27me3MAdult8wksC57bl6StdSig	Heart 8w H3K27m3	bigWig 0.140000 52.110001	Heart 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	98	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 8w H3K27m3\
subGroups view=Signal age=A1DLT8W factor=H3K27ME3 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k27me3MAdult8wksC57bl6StdSig\
type bigWig 0.140000 52.110001\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep1	Kidney - 1	bigWig 1.000000 742879.000000	Kidney A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	98	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel Kidney - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=KIDNEY rep=rep1\
track wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep1\
type bigWig 1.000000 742879.000000\

wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6MinusRawRep1	Lung 8w MR 1	bigWig 1.000000 66891.000000	Lung Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	98	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Lung 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LUNG localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 66891.000000\

wgEncodeSydhTfbsMelJundIggrabPk	MEL JunD	narrowPeak	MEL JunD TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	98	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL JunD TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL JunD\
subGroups view=Peaks factor=JUND cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelJundIggrabPk\
type narrowPeak\

wgEncodeUwDnaseFlbudCd1ME11halfSigRep1	Fore Limb Bud S 1	bigWig 1.000000 58871.000000	Fore Limb Bud DNaseI HS Signal Rep 1 from ENCODE/UW	2	99	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Fore Limb Bud DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Fore Limb Bud S 1\
subGroups view=Signal age=E11HALF cellType=FLBUD sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseFlbudCd1ME11halfSigRep1\
type bigWig 1.000000 58871.000000\

wgEncodeLicrHistoneHeartH3k36me3MAdult8wksC57bl6StdPk	Heart 8w H3K36m3	broadPeak	Heart 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	99	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 8w H3K36m3\
subGroups view=Peaks age=A1DLT8W factor=H3K36ME3 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k36me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep1	Kidney + 1	bigWig 1.000000 964197.000000	Kidney A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	99	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Kidney + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=KIDNEY rep=rep1\
track wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep1\
type bigWig 1.000000 964197.000000\

wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6PlusRawRep1	Lung 8w PR 1	bigWig 1.000000 672685.000000	Lung Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	99	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Lung 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LUNG localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 672685.000000\

wgEncodeSydhTfbsMelJundIggrabSig	MEL JunD	bigWig 1.000000 71501.000000	MEL JunD TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	99	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL JunD TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL JunD\
subGroups view=Signal factor=JUND cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelJundIggrabSig\
type bigWig 1.000000 71501.000000\

est	Mouse ESTs	psl est	Mouse ESTs Including Unspliced	0	100	0	0	0	127	127	127	1	0	0			<h2>Description</h2>\
\
<p>\
This track shows alignments between mouse expressed sequence tags\
(ESTs) in <a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">\
GenBank</a> and the genome. ESTs are single-read sequences,\
typically about 500 bases in length, that usually represent fragments of\
transcribed genes.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track follows the display conventions for\
<a href="../goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank">\
PSL alignment tracks</a>. In dense display mode, the items that\
are more darkly shaded indicate matches of better quality.\
</p>\
\
<p>\
The strand information (+/-) indicates the\
direction of the match between the EST and the matching\
genomic sequence.  It bears no relationship to the direction\
of transcription of the RNA with which it might be associated.\
</p>\
\
<p>\
The description page for this track has a filter that can be used to change\
the display mode, alter the color, and include/exclude a subset of items\
within the track. This may be helpful when many items are shown in the track\
display, especially when only some are relevant to the current task.\
</p>\
\
<p>\
To use the filter:\
<ol>\
<li>Type a term in one or more of the text boxes to filter the EST\
display. For example, to apply the filter to all ESTs expressed in a specific\
organ, type the name of the organ in the tissue box. To view the list of\
valid terms for each text box, consult the table in the Table Browser that\
corresponds to the factor on which you wish to filter. For example, the\
&quot;tissue&quot; table contains all the types of tissues that can be\
entered into the tissue text box. Multiple terms may be entered at once,\
separated by a space. Wildcards may also be used in the filter.</li>\
<li>If filtering on more than one value, choose the desired combination\
logic. If &quot;and&quot; is selected, only ESTs that match all filter\
criteria will be highlighted. If &quot;or&quot; is selected, ESTs that\
match any one of the filter criteria will be highlighted.</li>\
<li>Choose the color or display characteristic that should be used to\
highlight or include/exclude the filtered items. If &quot;exclude&quot; is\
chosen, the browser will not display ESTs that match the filter criteria.\
If &quot;include&quot; is selected, the browser will display only those\
ESTs that match the filter criteria.</li>\
</ol>\
</p>\
\
<p>\
This track may also be configured to display base labeling, a feature that\
allows the user to display all bases in the aligning sequence or only those\
that differ from the genomic sequence. For more information about this option,\
go to the\
<a href="../goldenPath/help/hgBaseLabel.html" target="_blank">\
Base Coloring for Alignment Tracks</a> page.\
Several types of alignment gap may also be colored;\
for more information, go to the\
<a href="../goldenPath/help/hgIndelDisplay.html" target="_blank">\
Alignment Insertion/Deletion Display Options</a> page.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
To make an EST, RNA is isolated from cells and reverse\
transcribed into cDNA.  Typically, the cDNA is cloned\
into a plasmid vector and a read is taken from the 5'\
and/or 3' primer.  For most &mdash; but not all &mdash; ESTs, the\
reverse transcription is primed by an oligo-dT, which\
hybridizes with the poly-A tail of mature mRNA. The\
reverse transcriptase may or may not make it to the 5'\
end of the mRNA,  which may or may not be degraded.\
</p>\
\
<p>\
In general, the 3' ESTs mark the end of transcription\
reasonably well, but the 5' ESTs may end at any point\
within the transcript.  Some of the newer cap-selected\
libraries cover transcription start reasonably well. Before the\
cap-selection techniques\
emerged, some projects used random rather than poly-A\
priming in an attempt to retrieve sequence distant from the\
3' end.  These projects were successful at this, but as\
a side effect also deposited sequences from unprocessed\
mRNA and perhaps even genomic sequences into the EST databases.\
Even outside of the random-primed projects, there is a\
degree of non-mRNA contamination. Because of this, a\
single unspliced EST should be viewed with considerable\
skepticism.\
</p>\
\
<p>\
To generate this track, mouse ESTs from GenBank were aligned\
against the genome using blat. Note that the maximum intron length\
allowed by blat is 750,000 bases, which may eliminate some ESTs with very\
long introns that might otherwise align. When a single\
EST aligned in multiple places, the alignment having the\
highest base identity was identified.  Only alignments having\
a base identity level within 0.5% of the best and at least 96% base identity\
with the genomic sequence were kept.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
This track was produced at UCSC from EST sequence data\
submitted to the international public sequence databases by\
scientists worldwide.\
</p>\
\
<h2>References</h2>\
<p>\
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.\
<a href="https://academic.oup.com/nar/article/41/D1/D36/1068219/GenBank" target="_blank">\
GenBank</a>.\
<em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D36-42.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23193287" target="_blank">23193287</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531190/" target="_blank">PMC3531190</a>\
</p>\
\
<P>\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
<A HREF="https://academic.oup.com/nar/article/32/suppl_1/D23/2505202/GenBank-update"\
TARGET=_blank>GenBank: update</A>.\
<em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D23-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681350" target="_blank">14681350</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308779/" target="_blank">PMC308779</a>\
</p>\
\
<P>\
Kent WJ.\
<A HREF="https://genome.cshlp.org/content/12/4/656.abstract" \
TARGET=_blank>BLAT - the BLAST-like alignment tool</A>.\
<em>Genome Res</em>. 2002 Apr;12(4):656-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a>\
</p>\
	rna	1	baseColorUseSequence genbank\
group rna\
indelDoubleInsert on\
indelQueryInsert on\
intronGap 30\
longLabel Mouse ESTs Including Unspliced\
maxItems 300\
shortLabel Mouse ESTs\
spectrum on\
table all_est\
track est\
type psl est\
visibility hide\

mrna	Mouse mRNAs	psl .	Mouse mRNAs from GenBank	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
\
<p>\
The mRNA track shows alignments between mouse mRNAs\
in <a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">\
GenBank</a> and the genome.</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track follows the display conventions for\
<a href="../goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank">\
PSL alignment tracks</a>. In dense display mode, the items that\
are more darkly shaded indicate matches of better quality.\
</p>\
\
<p>\
The description page for this track has a filter that can be used to change\
the display mode, alter the color, and include/exclude a subset of items\
within the track. This may be helpful when many items are shown in the track\
display, especially when only some are relevant to the current task.\
</p>\
\
<p>\
To use the filter:\
<ol>\
<li>Type a term in one or more of the text boxes to filter the mRNA\
display. For example, to apply the filter to all mRNAs expressed in a specific\
organ, type the name of the organ in the tissue box. To view the list of\
valid terms for each text box, consult the table in the Table Browser that\
corresponds to the factor on which you wish to filter. For example, the\
&quot;tissue&quot; table contains all the types of tissues that can be\
entered into the tissue text box. Multiple terms may be entered at once,\
separated by a space. Wildcards may also be used in the filter.</li>\
<li>If filtering on more than one value, choose the desired combination\
logic. If &quot;and&quot; is selected, only mRNAs that match all filter\
criteria will be highlighted. If &quot;or&quot; is selected, mRNAs that\
match any one of the filter criteria will be highlighted.</li>\
<li>Choose the color or display characteristic that should be used to\
highlight or include/exclude the filtered items. If &quot;exclude&quot; is\
chosen, the browser will not display mRNAs that match the filter criteria.\
If &quot;include&quot; is selected, the browser will display only those\
mRNAs that match the filter criteria.</li>\
</ol>\
</p>\
\
<p>\
This track may also be configured to display codon coloring, a feature that\
allows the user to quickly compare mRNAs against the genomic sequence. For more\
information about this option, go to the\
<a href="../goldenPath/help/hgCodonColoringMrna.html" target="_blank">\
Codon and Base Coloring for Alignment Tracks</a> page.\
Several types of alignment gap may also be colored;\
for more information, go to the\
<a href="../goldenPath/help/hgIndelDisplay.html" target="_blank">\
Alignment Insertion/Deletion Display Options</a> page.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
GenBank mouse mRNAs were aligned against the genome using the\
blat program. When a single mRNA aligned in multiple places,\
the alignment having the highest base identity was found.\
Only alignments having a base identity level within 0.5% of\
the best and at least 96% base identity with the genomic sequence were kept.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
The mRNA track was produced at UCSC from mRNA sequence data\
submitted to the international public sequence databases by\
scientists worldwide.\
</p>\
\
<h2>References</h2>\
<p>\
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.\
<a href="https://academic.oup.com/nar/article/41/D1/D36/1068219/GenBank" target="_blank">\
GenBank</a>.\
<em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D36-42.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23193287" target="_blank">23193287</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531190/" target="_blank">PMC3531190</a>\
</p>\
\
<P>\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
<A HREF="https://academic.oup.com/nar/article/32/suppl_1/D23/2505202/GenBank-update"\
TARGET=_blank>GenBank: update</A>.\
<em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D23-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681350" target="_blank">14681350</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308779/" target="_blank">PMC308779</a>\
</p>\
\
<P>\
Kent WJ.\
<A HREF="https://genome.cshlp.org/content/12/4/656.abstract" \
TARGET=_blank>BLAT - the BLAST-like alignment tool</A>.\
<em>Genome Res</em>. 2002 Apr;12(4):656-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a>\
</p>\
	rna	1	baseColorDefault diffCodons\
baseColorUseCds genbank\
baseColorUseSequence genbank\
group rna\
indelDoubleInsert on\
indelPolyA on\
indelQueryInsert on\
longLabel Mouse mRNAs from GenBank\
shortLabel Mouse mRNAs\
showDiffBasesAllScales .\
table all_mrna\
track mrna\
type psl .\
visibility hide\

acembly	AceView Genes	genePred acemblyPep acemblyMrna	AceView Gene Models With Alt-Splicing	0	100	155	0	125	205	127	190	0	0	0		https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=mouse&l=$$	<H2>Description</H2>\
<P>\
This track shows <A HREF="https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/" \
TARGET=_BLANK>AceView</A> gene models constructed from\
cDNA and genomic evidence by Danielle and Jean Thierry-Mieg\
using the <A HREF="https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/"\
TARGET=_blank>Acembly</A> program.</P> \
\
<P>\
AceView is the only database that defines the genes\
genome-wide by using only, but exhaustively, the public experimental\
cDNA sequences from the same species.  The analysis relies on the\
quality of the genome sequence and exploits sophisticated cDNA-to-genome \
co-alignment algorithms to provide a comprehensive and\
non-redundant representation of the GenBank, dbEST, GSS, Trace and\
RefSeq cDNA sequences. In a way, the AceView transcripts represent a\
fully annotated non-redundant &lsquo;nr&rsquo; view of the public\
RNAs, minus cloning artefacts, contaminations and bad quality\
sequences. AceView transcripts represent a 10 times compaction\
relative to the raw data, with minimal loss of sequence\
information.</P>\
\
<P>\
87% of the public RNA sequences are coalesced into AceView alternative\
transcripts and genes, thereby identifying close to twice as many main\
genes as there are &quot;known genes&quot; in both human and\
mouse. 18% to 25% of the spliced genes appear non-coding, in mouse and\
human respectively.  Alternative transcripts are prominent in both\
species. The typical human gene produces on average eight distinct\
alternatively spliced forms from three promoters and with three\
non-overlapping terminal exons. It has on average three cassette exons\
and four internal donor or acceptor sites.  The AceView site further\
proposes a thorough biological annotation of the reconstructed genes,\
including association to diseases and tissue specificity of the\
alternative transcripts.</P>\
\
<P>AceView combines respect for the experimental data with extensive\
quality control. Evaluated in the ENCODE regions, AceView transcripts\
are close to indistinguishable from the manually curated Gencode\
reference genes (see Thierry-Mieg, 2006, or compare the two tracks in the \
Genome Browser), but over the entire genome the number of transcripts exceeds\
Havana/Vega by a factor of three and RefSeq by a factor of six.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<P>\
This track follows the display conventions for \
<A HREF="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene \
tracks</A>. Gene models that fall into the &quot;main&quot; class\
are displayed in <font color="#80007D">purple</font>; &quot;putative&quot; \
genes are displayed in <font color="#C8007D" >pink</font>.</P>\
\
<P>The main genes include at least one transcript which is spliced or\
putatively protein coding. Spliced genes contain at least one\
well-defined standard intron, i.e., an intron with a GT-AG or GC-AG\
boundary, supported by at least one clone matching exactly, with no\
ambiguous bases, 8 bases of the genome on each side of the intron.</P>\
\
<P>The putative genes have no standard intron and do not encode good\
proteins, yet are supported by more than six cDNA clones.</P>\
\
<P>\
The track description page offers the following filter and configuration\
options:\
<UL>\
<LI><B>Gene Class filter:</B> Select the <em>main</em> or <em>putative</em>\
option to filter the display. \
<LI><B>Color track by codons:</B> Select the <em>genomic codons</em> option\
to color and label each codon in a zoomed-in display to facilitate validation \
and comparison to gene predictions. Click the \
<A HREF="../goldenPath/help/hgCodonColoring.html">Codon coloring help</A> link \
on the track description page for more information about this feature.\
</UL>\
</P>\
\
<H2>Methods</H2>\
<P>The millions of cDNA sequences available from the public databases\
(GenBank, dbEST, GSS, Traces, etc.) are aligned cooperatively on the\
genome sequence, taking care to keep the paired 5' and 3' reads from\
single clones associated in the same transcript. \
Useful information about tissue, stage, publications, isolation\
procedure and so on is gathered. </P>\
\
<P>AceView alignments on the genome use knowledge on sequencing errors\
gained from analyzing sequencing traces and cooperative\
refinements. They are usually obtained over the entire length of the\
EST or mRNA, (average 98.8% aligned, 0.2% mismatches in mRNAs or 95.5%\
aligned, 1.4% mismatches in ESTs). </P>\
\
<P>Multiple alignments are evaluated and the sequences are stringently\
kept only in their best position genome-wide. Less than 1% of the\
mRNAs and less than 2% of the ESTs will ultimately be aligned in more\
than one gene, usually in the ~1% closely repeated genes. </P>\
\
<P>The cDNA sequences are then processed and cleaned: the vectors and\
polyA are clipped, the reads submitted on the wrong strand are\
flipped, and the small insertion or deletion polymorphisms are\
identified.</P>\
\
<P>Eventual cDNA clone rearrangements or anomalous alignments are\
flagged and filtered (akin to manually) so as not to lose unique\
valuable information while avoiding pollution of the database with\
poorly supported anomalous data. </P>\
\
<P>Unfortunately, cDNA libraries are still far from saturation, so\
after 20% of the suspicious entries have been removed, a single good-quality\
cDNA sequence, aligned with standard introns on the genome, is\
considered sufficient evidence for a given mRNA structure. That is\
because cDNA sequences are difficult to obtain, but they remain the\
cleanest and most reliable information to best define the molecular\
genes. Unspliced non-coding genes are however reported (in the\
putative class) only if they are supported by six or more accessions. Others \
belong to what is termed &lsquo;the cloud&rsquo; (not displayed on\
the UCSC Genome Browser). </P>\
\
<P>The cDNA sequences are clustered into a minimal number of\
alternative transcript variants, preferring partial transcripts to\
artificially extended ones. Sequences are concatenated by simple\
contact, but the combinatorics are voided by allowing each cDNA\
accession to contribute to a single alternative variant, preferably\
one where it merges silently without bringing any new sequence\
information. As a result, for instance, all shorter reads compatible\
with a full-length mRNA will be absorbed in that transcript and will not \
be available to allow for extensions on other incompatible\
transcripts. </P>\
\
<P>About 70% of the variants, clearly identified on the Acembly site, have\
their entire coding region supported by a single cDNA; the others may\
be illicit concatenations that could be split when more data become\
available. </P>\
\
<P>For each transcript, the consensus sequence of the cDNAs most\
compatible to the genome sequence is generated. Single base insertion,\
deletion, transition or transversion is shown graphically in the mRNA\
view, where frequent SNPs become evident.</P>\
\
<P>The main sequence of the transcript used in the annotation is that\
of the footprint of the transcript on the genome, which is of better\
quality than the mRNAs: this procedure corrects up to 2% sequencing\
errors. </P>\
\
<P>Putative protein-coding regions are predicted from the mRNA\
sequence and annotated using BlastP, PFAM, Psort2, and comparison to\
AceView proteins from other species. Best proteins are scored (see the\
FAQ on the Acembly site) and transcripts are putatively proposed to be \
protein-coding or non-coding. </P>\
\
<P>Expression, cDNA support, tissue specificity, sequences of\
alternative transcripts, introns and exons, alternative promoters,\
alternative exons and alternative polyadenylation sites are evaluated\
and annotated on the Acembly web site. </P>\
\
<P>The reconstructed alternative transcripts are then grouped into\
genes if they share at least one exact intron boundary or if they have\
substantial sequence overlap. </P>\
\
<P>Coding and non-coding genes are defined, and genes in antisense are\
flagged. </P>\
\
<P>AceView genes are matched molecularly to Entrez genes and named\
according to the official nomenclature or the Entrez Gene\
nomenclature. For novel genes not in Entrez, AceView creates new gene\
names that are maintained from release to release until the genes receive\
an official or Entrez gene name. </P>\
\
<P>Each gene is annotated in depth, with the intention of AceView serving \
as a one-stop knowledgebase for systems biology. Selected functional\
annotations are gathered from various sources, including expression\
data, protein interactions and GO annotations. In particular, possible\
disease associations are extracted directly from PubMed, in addition\
to OMIM and GAD, and the users can help refine those annotations.</P>\
\
<P>Finally, lists of the most closely related genes by function,\
pathway, protein complex, GO annotation, disease, cellular\
localization or all criteria taken together are proposed, to\
stimulate research and development.</P>\
\
<P>Click the &quot;AceView Gene Summary&quot; on an individual transcript's\
details page to access the gene on the NCBI AceView website.</P>\
\
<H2>Credits</H2>\
<P>\
Thanks to \
<A HREF="mailto:&#109;&#105;&#101;g&#64;&#110;&#99;&#98;&#105;.\
&#110;&#108;&#109;.\
ni&#104;.\
&#103;&#111;&#118;">\
Danielle and Jean Thierry-Mieg</A> at NCBI for providing this track\
for human, worm and mouse.</P>\
\
<H2>References</H2>\
<p>\
Thierry-Mieg D, Thierry-Mieg J.\
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-s1-s12" target="_blank">\
AceView: a comprehensive cDNA-supported gene and transcripts annotation</a>.\
<em>Genome Biol</em>. 2006;7 Suppl 1:S12.1-14.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16925834" target="_blank">16925834</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810549/" target="_blank">PMC1810549</a>\
</p>\
\
<P>\
AceView web site:\
<A HREF="https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/" \
TARGET=_BLANK>https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly</A></P>\
\
	genes	1	autoTranslate 0\
color 155,0,125\
exonNumbers on\
gClass_main 128,0,125\
gClass_putative 200,0,125\
geneClasses main putative\
group genes\
itemClassTbl acemblyClass\
longLabel AceView Gene Models With Alt-Splicing\
shortLabel AceView Genes\
track acembly\
type genePred acemblyPep acemblyMrna\
url https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=mouse&l=$$\
urlLabel AceView Gene Summary:\
visibility hide\

affyAllExonSuper	Affy Exon		Affymetrix All Exon Microarrays	0	100	0	0	0	127	127	127	0	0	0			<H2>Overview</H2>\
This super-track combines related tracks of the Affymetrix All Exon chip data.\
There are two member tracks:\
<UL>\
<LI><B>Affymetrix Exon Array 1.0: Normal Tissues</B>: This track displays data\
from 11 different sample tissues across three replicate arrays each.\
</LI>\
<LI><B>Affymetrix Exon Array 1.0: Probesets</B>: This track displays probeset\
loci for the array.\
</LI>\
</UL>\
	regulation	0	group regulation\
longLabel Affymetrix All Exon Microarrays\
shortLabel Affy Exon\
superTrack on\
track affyAllExonSuper\

affyAllExonProbes	Affy Exon Probes	bed 6 .	Affymetrix Exon Array 1.0: Probesets	3	100	0	0	0	127	127	127	1	0	0			<H2>Description</H2>\
<P>\
The <A HREF="http://www.affymetrix.com/estore/products_services/arrays/index.affx"\
TARGET=_blank>Exon GeneChip</A> contains over one million probe \
sets\
designed to interrogate individual exons rather than the 3' ends of transcripts\
as in traditional GeneChips. Exons were derived from a variety of\
annotations that have been divided into the classes Core, Extended\
and Full. \
<UL> \
  <LI><B>Core:\
    </B>RefSeq transcripts, full-length GenBank mRNAs</LI>\
  <LI><B>Extended:</B> \
    dbEst alignments, Ensembl annotations, syntenic mRNA from human, rat and mouse, \
    microRNA annotations, MITOMAP annotations, Vega genes, Vega pseudogenes\
  <LI><B>Full:</B>\
    Geneid genes, Genscan genes, Genscan Subopt, Exoniphy, RNA genes, SGP genes,\
    Twinscan genes\
  </LI>\
</UL></P> \
\
<P>\
Probe sets are colored by class with the Core probe sets being\
the darkest and the Full being the lightest color. Additionally, probe\
sets that do not overlap the exons of a transcript cluster, but fall\
inside of its introns, are considered bounded by that transcript\
cluster and are colored slightly lighter. Probe sets that overlap the\
coding portion of the Core class are colored slightly darker.</P>\
<P>\
The microarray track using this probe set can be displayed by turning\
on the <B>Affy Exon Tissue</B> track.</P>\
\
<H2>Credits and References</H2>\
<P>\
The exons interrogated by the probe sets displayed in this track are\
from the Affymetrix Exon 1.0 GeneChip and were derived from a\
number of sources. In addition to the millions of cDNA sequences\
contributed to the \
<A HREF="https://www.ncbi.nlm.nih.gov/genbank/" \
TARGET=_blank>GenBank</A>, \
<A HREF="https://www.ncbi.nlm.nih.gov/dbEST/" TARGET=_blank>dbEst</A> and \
<A HREF="https://www.ncbi.nlm.nih.gov/refseq/" TARGET=_blank>RefSeq</A> \
databases by\
individual labs and scientists, the following annotations were used:\
<P>\
<A HREF="http://www.ensembl.org/index.html" \
TARGET=_blank><B>Ensembl</B></A><B>: </B>\
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T <em>et\
al</em>.\
<a href="https://academic.oup.com/nar/article/30/1/38/1332872" target="_blank">\
The Ensembl genome database project</a>.\
<em>Nucleic Acids Res</em>. 2002 Jan 1;30(1):38-41.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11752248" target="_blank">11752248</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99161/" target="_blank">PMC99161</a>\
</p>\
\
<P>\
<a href="http://compgen.cshl.edu/phast/" target"_blank"><B>Exoniphy</a>:</B> Siepel, A., Haussler, D. \
<A HREF="http://compgen.cshl.edu/~acs/recomb2004.pdf"\
TARGET=_blank>Computational identification of evolutionarily conserved \
exons</A>.\
<em>Proc. 8th Int'l Conf. on Research in Computational Molecular Biology</em>, \
177-186 (2004).\
</P>\
\
<P>\
<B><A HREF="https://genome.crg.es/geneid.html" TARGET=_blank>Geneid Genes</A>:</B>\
Parra G, Blanco E, Guig&#243; R.\
<a href="https://genome.cshlp.org/content/10/4/511.abstract" target="_blank">\
GeneID in Drosophila</a>.\
<em>Genome Res</em>. 2000 Apr;10(4):511-5.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10779490" target="_blank">10779490</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310871/" target="_blank">PMC310871</a>\
</p>\
\
<P>\
<B><A HREF="http://hollywood.mit.edu/GENSCAN.html" TARGET=_blank>Genscan Genes</A>:</B> \
Burge C, Karlin S.\
<a href="https://www.sciencedirect.com/science/article/pii/S0022283697909517" target="_blank">\
Prediction of complete gene structures in human genomic DNA</a>.\
<em>J Mol Biol</em>. 1997 Apr 25;268(1):78-94.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/9149143" target="_blank">9149143</a>\
</p>\
\
<P>\
<B><A HREF="https://www.mirbase.org/" TARGET=_blank>microRNA</A>:</B>\
Griffiths-Jones S.\
<a href="https://academic.oup.com/nar/article/32/suppl_1/D109/2505171" target="_blank">\
The microRNA Registry</a>.\
<em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D109-11.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681370" target="_blank">14681370</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308757/" target="_blank">PMC308757</a>\
</p>\
\
<P>\
<B><A HREF="https://www.mitomap.org//MITOMAP" TARGET=_blank>MITOMAP</A>:</B>\
Kogelnik AM, Lott MT, Brown MD, Navathe SB, Wallace DC.\
<a href="https://academic.oup.com/nar/article/33/suppl_1/D611/2505354" target="_blank">\
MITOMAP: a human mitochondrial genome database</a>.\
<em>Nucleic Acids Res</em>. 1996 Jan 1;24(1):177-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8594574" target="_blank">8594574</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC145607/" target="_blank">PMC145607</a>\
</p>\
\
<P>\
<B><A HREF="http://eddylab.org" TARGET=_blank>RNA Genes</A>:</B>\
Lowe TM, Eddy SR.\
<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/pdf/250955.pdf" target="_blank">\
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence</a>.\
<em>Nucleic Acids Res</em>. 1997 Mar 1;25(5):955-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/9023104" target="_blank">9023104</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/" target="_blank">PMC146525</a>\
</p>\
\
<P>\
<B><A HREF="http://grib.imim.es" TARGET=_blank>SGP Genes</A>: </B> \
Wiehe T, Gebauer-Jung S, Mitchell-Olds T, Guig&#243; R.\
<a href="https://genome.cshlp.org/content/11/9/1574.full" target="_blank">\
SGP-1: prediction and validation of homologous genes based on sequence alignments</a>.\
<em>Genome Res</em>. 2001 Sep;11(9):1574-83.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11544202" target="_blank">11544202</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311140/" target="_blank">PMC311140</a>\
</p>\
\
<P>\
<B><A HREF="https://mblab.wustl.edu/" TARGET=_blank>Twinscan Genes</A>:</B>\
Korf I, Flicek P, Duan D, Brent MR.\
<a href="https://academic.oup.com/bioinformatics/article/17/suppl_1/S140/261903" target="_blank">\
Integrating genomic homology into gene structure prediction</a>.\
<em>Bioinformatics</em>. 2001;17 Suppl 1:S140-8.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11473003" target="_blank">11473003</a>\
</p>\
\
<P>\
<B><A HREF="http://vega.archive.ensembl.org/index.html" TARGET=_blank>Vega Genes \
and Pseudogenes</A>: </B>The HAVANA group, \
<A HREF="https://www.sanger.ac.uk/" TARGET=_blank>Wellcome Trust Sanger \
Institute</A>.</P>\
	regulation	1	exonArrows on\
group regulation\
longLabel Affymetrix Exon Array 1.0: Probesets\
shortLabel Affy Exon Probes\
spectrum on\
superTrack affyAllExonSuper dense\
track affyAllExonProbes\
type bed 6 .\
useScore 1\
visibility pack\

affyExonTissues	Affy Exon Tissues	expRatio	Affymetrix Exon Array 1.0: Normal Tissues	2	100	0	0	0	127	127	127	0	0	0			<H2>Methods</H2>\
<P>\
RNA (from a commercial source) from 11 tissues were hybridized to Affymetrix \
Mouse Exon 1.0 ST arrays. For each tissue, 3 replicate experiments were \
performed \
for a total of 33 arrays.  The raw intensity signal from the arrays\
was normalized\
with a quantile normalization method, then run through the PLIER algorithm.\
The normalized data were then converted to median-centered log-ratios, \
which are displayed as green for negative log-ratios (below-median expression),\
and red for positive (above-median expression).</P>\
\
<P>The probe sets for this microarray track are shown in the \
the <B>Affy Exon Probes</B> track.</P>\
\
<H2>Credits</H2>\
<P>\
This track was produced by Andy Pohl, Kayla Smith, and Pauline Fujita of the \
genome browser group at UCSC, Melissa Cline of the \
<A HREF="http://ribonode.ucsc.edu/" TARGET=_blank>Ares lab</A> at UCSC, and \
Chuck Sugnet at <A HREF="https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html" TARGET=_blank>Affymetrix</A>, based on \
<A HREF="https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/microarray-analysis-sample-data/exon-st-array-sample-data-set.html" target="_blank">\
sample exon array data</A> available from Affymetrix, produced by Tyson Clark. \
</P>\
\
<H2>References</H2>\
<p>\
Pohl AA, Sugnet CW, Clark TA, Smith K, Fujita PA, Cline MS.\
<a href="https://academic.oup.com/bioinformatics/article/25/18/2442/197035" target="_blank">\
Affy exon tissues: exon levels in normal tissues in human, mouse and rat</a>.\
<em>Bioinformatics</em>. 2009 Sep 15;25(18):2442-3.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19570805" target="_blank">19570805</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735668/" target="_blank">PMC2735668</a>\
</p>\
\
<H2>Links</H2>\
<P><UL><LI>\
<A HREF="https://www.thermofisher.com/order/catalog/product/901168"\
target="_blank">Affymetrix Mouse Exon 1.0 ST array web page</A></LI>\
<LI><A HREF="https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/microarray-analysis-sample-data/exon-st-array-sample-data-set.html" target="_blank"\
>Affymetrix Mouse Exon data</A></LI>\
<LI><A HREF="http://tools.thermofisher.com/content/sfs/brochures/plier_technote.pdf" target="_blank"\
>PLIER algorithm documentation (PDF).</A></LI></UL></P>\
	regulation	1	expScale 3.0\
expStep 0.5\
expTable affyExonTissuesExps\
group regulation\
groupings affyExonTissuesGroups\
longLabel Affymetrix Exon Array 1.0: Normal Tissues\
shortLabel Affy Exon Tissues\
superTrack affyAllExonSuper dense\
track affyExonTissues\
type expRatio\
visibility full\

affyGnf1m	Affy GNF1M	psl .	Alignments of Probes from Affymetrix GNF1M Chip	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track shows the location of the sequences used for the selection of \
probes on the Affymetrix GNF1M chips. The annotation contains 31,000 \
non-overlapping mouse genes and gene predictions.</P>\
\
<H2>Methods</H2>\
<P>\
The sequences were mapped to the genome with blat followed by pslReps \
using the parameters <TT>-minCover=0.3</TT>, <TT>-minAli=0.95</TT> and \
<TT>-nearTop=0.005</TT>.  </P>\
\
<H2>Credits</H2>\
<P>\
Thanks to the \
<A HREF="https://www.gnf.nibr.com/" TARGET=_blank>Genomics Institute of the Novartis\
Research Foundation</A> (GNF) for the data underlying this track.  </P>\
	regulation	1	group regulation\
longLabel Alignments of Probes from Affymetrix GNF1M Chip\
shortLabel Affy GNF1M\
track affyGnf1m\
type psl .\
visibility hide\

affyMOE430	Affy MOE430	psl .	Alignments of Affymetrix Consensus Sequences from Mouse MOE430 (A and B)	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track shows the location of the consensus sequences used for the \
selection of probes on the Affymetrix Mouse MOE430 set (A and B) of chips.</P>\
\
<H2>Methods</H2>\
<P>\
Consensus sequences were downloaded from the\
<A HREF="http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430"\
TARGET = _BLANK>Affymetrix Product Support</A>\
and mapped to the genome with blat followed by pslReps using the parameters\
<TT>-minCover=0.3</TT>, <TT>-minAli=0.95</TT> and <TT>-nearTop=0.005</TT>.</P>\
\
<H2>Credits</H2>\
<P>\
Thanks to <A HREF="https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html" TARGET=_blank>Affymetrix</A> \
for the data underlying this track.</P>\
\
	regulation	1	group regulation\
longLabel Alignments of Affymetrix Consensus Sequences from Mouse MOE430 (A and B)\
shortLabel Affy MOE430\
track affyMOE430\
type psl .\
visibility hide\

affyU74	Affy U74	psl .	Alignments of Affymetrix Consensus Sequences from MG-U74 v2 (A,B, and C)	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track shows the location of the consensus sequences used for the \
selection of probes on the Affymetrix MG-U74v2 set (A,B and C) of chips.</P>\
\
<H2>Methods</H2>\
<P>\
Consensus sequences were downloaded from the\
<A HREF="http://www.affymetrix.com/support/technical/byproduct.affx?product=mgu74"\
TARGET = _BLANK>Affymetrix Product Support</A>\
and mapped to the genome with blat followed by pslReps using the parameters\
<TT>-minCover=0.3</TT>, <TT>-minAli=0.95</TT> and <TT>-nearTop=0.005</TT>.</P>\
\
<H2>Credits</H2>\
<P>\
Thanks to <A HREF="https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html" TARGET=_blank>Affymetrix</A> \
for the data underlying this track.</P>\
	regulation	1	group regulation\
longLabel Alignments of Affymetrix Consensus Sequences from MG-U74 v2 (A,B, and C)\
shortLabel Affy U74\
track affyU74\
type psl .\
visibility hide\

genotypeArrays	Agilent CGH	bed 3	Agilent CGH Microarray probesets	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track displays the probes from the \
<A HREF="https://www.genomics.agilent.com/en/CGH-CGH-SNP-Microarrays/?pgid=AG-PG-9"\
TARGET=_blank>Agilent Catalog Oligonucleotide Microarrays</A>.\
</P>\
<P>\
Agilent's oligonucleotide CGH (Comparative Genomic Hybridization) platform enables\
the study of genome-wide DNA copy number changes at a high resolution. The probes\
on Agilent aCGH microarrays are 60-mer oligonucleotides synthesized in situ using\
Agilent's inkjet SurePrint technology. The probes represented on the Agilent CGH\
microarrays have been selected using algorithms developed specifically for the\
CGH application, assuring optimal performance of these probes in detecting DNA\
copy number changes.\
</P>\
<P>\
The Agilent catalog CGH microarrays are printed on 1 in. x 3 in. glass slides\
and are available in several formats. \
The mouse catalog SurePrint G3 microarrays formats are the 1x1M and 4x180K.\
The legacy mouse catalog SurePrint HD microarrays are the 1x244K and 2x105K.\
</P>\
<p>\
Subtracks were colored in alternating shades of green and orange to highlight track boundaries. \
This track consists of the following subtracks:\
</P>\
<P>\
<TABLE><TR><TD BGCOLOR=#888888> \
<TABLE CELLSPACING=1 CELLPADDING=3>\
<TR> \
<TD BGCOLOR="#1616D1"><FONT COLOR="#FFFFFF"><B>Description</B></FONT></TD>\
<TD BGCOLOR="#1616D1"><FONT COLOR="#FFFFFF"><B>AMADID</B></FONT></TD>\
<TD BGCOLOR="#1616D1"><FONT COLOR="#FFFFFF"><B>Samples per Slide</B></FONT></TD>\
<TD BGCOLOR="#1616D1"><FONT COLOR="#FFFFFF"><B>Biological Features</B></FONT></TD>\
<TD BGCOLOR="#1616D1"><FONT COLOR="#FFFFFF"><B>Median Probe Spacing</B></FONT></TD>\
<TD BGCOLOR="#1616D1"><FONT COLOR="#FFFFFF"><B>Gene-biased</B></FONT></TD>\
</TR>\
<TR>\
<TD BGCOLOR="#D9F8E4">SurePrint G3 Mouse CGH Microarray 1x1M</TD>\
<TD BGCOLOR="#D9F8E4">027414</TD>\
<TD BGCOLOR="#D9F8E4">1</TD>\
<TD BGCOLOR="#D9F8E4">967,265</TD>\
<TD BGCOLOR="#D9F8E4">1.8 kb</TD>\
<TD BGCOLOR="#D9F8E4">Yes</TD>\
</TR>\
<TR>\
<TD BGCOLOR="#D9E4FF">SurePrint G3 Mouse CGH Microarray 4x180K</TD>\
<TD BGCOLOR="#D9E4FF">027411</TD>\
<TD BGCOLOR="#D9E4FF">4</TD>\
<TD BGCOLOR="#D9E4FF">174,307</TD>\
<TD BGCOLOR="#D9E4FF">11 kb</TD>\
<TD BGCOLOR="#D9E4FF">Yes</TD>\
</TR>\
<TR>\
<TD BGCOLOR="#D9F8E4">SurePrint HD Mouse CGH Microarray 1x244K</TD>\
<TD BGCOLOR="#D9F8E4">014695</TD>\
<TD BGCOLOR="#D9F8E4">1</TD>\
<TD BGCOLOR="#D9F8E4">235,188</TD>\
<TD BGCOLOR="#D9F8E4">7.8 kb</TD>\
<TD BGCOLOR="#D9F8E4">Yes</TD>\
</TR>\
<TR>\
<TD BGCOLOR="#D9E4FF">SurePrint HD Mouse CGH Microarray 2x105K</TD>\
<TD BGCOLOR="#D9E4FF">014699</TD>\
<TD BGCOLOR="#D9E4FF">2</TD>\
<TD BGCOLOR="#D9E4FF">98,510</TD>\
<TD BGCOLOR="#D9E4FF">19 kb</TD>\
<TD BGCOLOR="#D9E4FF">Yes</TD>\
</TR>\
</TABLE>\
</TD>\
</TR>\
</TABLE>\
</P>\
\
<H2>References</H2>\
<P>\
More information on the Agilent Oligonucleotide Microarrays is\
available \
<A HREF="https://www.genomics.agilent.com/en/CGH-CGH-SNP-Microarrays/?pgid=AG-PG-9"\
TARGET=_blank>here</A>.\
</P>\
<p>\
Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer\
PS <em>et al</em>.\
<a href="https://www.pnas.org/content/101/51/17765" target="_blank">\
Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2004 Dec 21;101(51):17765-70.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15591353" target="_blank">15591353</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC535426/" target="_blank">PMC535426</a>\
</p>\
<H2>Credits</H2>\
<P>\
Thanks to Shane Giles, Peter Webb, and Anniek De Witte from Agilent\
Technologies for providing these data.\
</P>\
	varRep	1	compositeTrack on\
group varRep\
longLabel Agilent CGH Microarray probesets\
noInherit on\
shortLabel Agilent CGH\
track genotypeArrays\
type bed 3\
visibility hide\

wgEncodeLicrRnaSeqViewAlignments	Alignments	bam	RNA-seq from ENCODE/LICR	0	100	0	0	0	127	127	127	0	0	0				regulation	1	bamColorMode off\
bamGrayMode aliQual\
baseColorDefault diffBases\
baseColorUseSequence lfExtra\
indelDoubleInsert on\
indelQueryInsert on\
longLabel RNA-seq from ENCODE/LICR\
maxWindowToDraw 1000000\
noColorTag .\
pairEndsByName on\
parent wgEncodeLicrRnaSeq\
shortLabel Alignments\
showDiffBasesAllScales .\
showDiffBasesMaxZoom 100\
showNames \
track wgEncodeLicrRnaSeqViewAlignments\
type bam\
view Alignments\
visibility hide\

wgEncodeSydhRnaSeqViewAlignments	Alignments	bam	RNA-seq from ENCODE/Stanford/Yale	1	100	0	0	0	127	127	127	0	0	0				regulation	1	bamColorMode off\
bamGrayMode aliQual\
baseColorDefault diffBases\
baseColorUseSequence lfExtra\
indelDoubleInsert on\
indelQueryInsert on\
longLabel RNA-seq from ENCODE/Stanford/Yale\
maxWindowToDraw 1000000\
noColorTag .\
pairEndsByName on\
parent wgEncodeSydhRnaSeq\
shortLabel Alignments\
showDiffBasesAllScales .\
showDiffBasesMaxZoom 100\
showNames off\
track wgEncodeSydhRnaSeqViewAlignments\
type bam\
view Alignments\
visibility dense\

wgEncodeCaltechRnaSeqViewAlignments	Alignments	bam	RNA-seq from ENCODE/Caltech	0	100	0	0	0	127	127	127	0	0	0				regulation	1	bamColorMode off\
bamGrayMode aliQual\
baseColorDefault diffBases\
baseColorUseSequence lfExtra\
indelDoubleInsert on\
indelQueryInsert on\
longLabel RNA-seq from ENCODE/Caltech\
maxWindowToDraw 1000000\
noColorTag .\
pairEndsByName on\
parent wgEncodeCaltechRnaSeq\
shortLabel Alignments\
showDiffBasesAllScales .\
showDiffBasesMaxZoom 100\
showNames \
track wgEncodeCaltechRnaSeqViewAlignments\
type bam\
view Alignments\
visibility hide\

wgEncodeCshlLongRnaSeqViewAlignments	Alignments	bam	Long RNA-seq from ENCODE/Cold Spring Harbor Lab	0	100	0	0	0	127	127	127	0	0	0				regulation	1	bamGrayMode aliQual\
indelDoubleInsert on\
indelQueryInsert on\
longLabel Long RNA-seq from ENCODE/Cold Spring Harbor Lab\
maxWindowToDraw 1000000\
pairEndsByName on\
parent wgEncodeCshlLongRnaSeq\
shortLabel Alignments\
showDiffBasesAllScales .\
showDiffBasesMaxZoom 100\
showNames on\
track wgEncodeCshlLongRnaSeqViewAlignments\
type bam\
view Alignments\
visibility hide\

wgEncodeUwRnaSeqViewAlignments	Alignments	bam	RNA-seq from ENCODE/UW	0	100	0	0	0	127	127	127	0	0	0				regulation	1	bamColorMode \
bamGrayMode aliQual\
baseColorDefault diffBases\
baseColorUseSequence lfExtra\
indelDoubleInsert on\
indelQueryInsert on\
longLabel RNA-seq from ENCODE/UW\
maxWindowToDraw 1000000\
noColorTag .\
pairEndsByName on\
parent wgEncodeUwRnaSeq\
shortLabel Alignments\
showDiffBasesAllScales .\
showDiffBasesMaxZoom 100\
showNames \
track wgEncodeUwRnaSeqViewAlignments\
type bam\
view Alignments\
visibility hide\

wgEncodePsuRnaSeqViewAlignments	Alignments	bam	RNA-seq from ENCODE/PSU	0	100	0	0	0	127	127	127	0	0	0				regulation	1	bamGrayMode aliQual\
baseColorDefault diffBases\
baseColorUseSequence lfExtra\
indelDoubleInsert on\
indelQueryInsert on\
longLabel RNA-seq from ENCODE/PSU\
maxWindowToDraw 1000000\
noColorTag .\
pairEndsByName on\
parent wgEncodePsuRnaSeq\
shortLabel Alignments\
showDiffBasesAllScales .\
showDiffBasesMaxZoom 100\
showNames on\
track wgEncodePsuRnaSeqViewAlignments\
type bam\
view Alignments\
visibility hide\

allenBrainAli	Allen Brain	psl .	Allen Brain Atlas Probes	0	100	50	0	100	152	127	177	0	0	0			<H2>Description</H2>\
<P>\
This track provides a link into the \
<A HREF="http://portal.brain-map.org/" TARGET=_blank> Allen Brain Atlas</A> (ABA)\
images for this probe.  The ABA is an extensive\
database of high resolution in-situ hybridization images of adult\
male mouse brains covering the majority of genes.</P>\
\
<H2>Methods</H2>\
<P>\
The ABA created a platform for high-throughput <em>in situ</em> hybridization \
(ISH) that allows a highly systematic approach to analyzing gene expression in \
the brain. ISH is a technique that allows the cellular localization of mRNA \
transcripts for specific genes. Labeled antisense probes, specific to a \
particular gene, are hybridized to cellular (sense) transcripts and subsequent \
detection of the bound probe produces specific labeling in those cells \
expressing the particular gene. This method involves tagged nucleotides \
detected by colorimetric methods.</P>\
\
<P>The platform used for the ABA utilizes this non-isotopic approach, with \
digoxigenin-labeled nucleotides incorporated into a riboprobe produced by <em>in\
vitro</em> transcription. This method produces a label that fills the cell body,\
in contrast to autoradiography that produces scattered silver grains surrounding\
each labeled cell. To enhance the ability to detect low level expression, the \
ABA has incorporated a tyramide signal amplification step into the protocol that\
greatly increases sensitivity. The specific methodology is described in detail \
within the <A HREF="http://help.brain-map.org/display/mousebrain/Documentation"\
TARGET=_blank>ABA Data Production Processes document</A>.</P>\
\
<H2>Credits</H2>\
<P>\
Thanks to the <A HREF="https://alleninstitute.org/" TARGET=_blank>Allen \
Institute for Brain Science</A> in general, and Susan \
Sunkin in particular, for coordinating with UCSC on this annotation.</P>\
\
	regulation	1	color 50,0,100\
group regulation\
longLabel Allen Brain Atlas Probes\
shortLabel Allen Brain\
track allenBrainAli\
type psl .\
visibility hide\

gold	Assembly	bed 3 +	Assembly from Fragments	0	100	150	100	30	230	170	40	0	0	0			<H2>Description</H2>\
<P>\
This track shows the draft assembly of the mouse genome.  \
Whole-genome shotgun reads were assembled into contigs.  When possible, \
contigs were grouped into scaffolds (also known as &quot;supercontigs&quot;).\
The order, orientation and gap sizes between contigs within a scaffold are\
based on paired-end read evidence. </P>\
<P>\
In dense mode, this track depicts the contigs that make up the \
currently viewed scaffold. \
Contig boundaries are distinguished by the use of alternating gold and brown \
coloration. Where gaps\
exist between contigs, spaces are shown between the gold and brown\
blocks.  The relative order and orientation of the contigs\
within a scaffold is always known; therefore, a line is drawn in the graphical\
display to bridge the blocks.</P>\
<P>\
Clone Type Key:\
<UL>\
<li><b>W</b> - Whole Genome Shotgun contig </li>\
<li><b>F</b> - Finished </li>\
<li><b>A</b> - In Active Finishing </li>\
<li><b>D</b> - Draft </li>\
</UL>\
</P>\
	map	1	altColor 230,170,40\
color 150,100,30\
group map\
longLabel Assembly from Fragments\
shortLabel Assembly\
track gold\
type bed 3 +\
visibility hide\

augustusGene	AUGUSTUS	genePred	AUGUSTUS ab initio gene predictions v3.1	0	100	12	105	0	133	180	127	0	0	0			<h2>Description</h2>\
\
<p>\
  This track shows <i>ab initio</i> predictions from the program\
  <a href="http://bioinf.uni-greifswald.de/augustus/" target="_blank">AUGUSTUS</a> (version 3.1).\
  The predictions are based on the genome sequence alone.\
</p>\
\
<p>\
For more information on the different gene tracks, see our <a target=_blank \
href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>\
\
<h2>Methods</h2>\
\
<p>\
Statistical signal models were built for splice sites, branch-point\
patterns, translation start sites, and the poly-A signal.\
Furthermore, models were built for the sequence content of\
protein-coding and non-coding regions as well as for the length distributions\
of different exon and intron types. Detailed descriptions of most of these different models\
can be found in Mario Stanke's\
<a href="https://ediss.uni-goettingen.de/handle/11858/00-1735-0000-0006-B3F8-4" target="_blank">dissertation</a>.\
This track shows the most likely gene structure according to a\
Semi-Markov Conditional Random Field model.\
Alternative splicing transcripts were obtained with\
a sampling algorithm (<tt>--alternatives-from-sampling=true --sample=100 --minexonintronprob=0.2\
--minmeanexonintronprob=0.5 --maxtracks=3 --temperature=2</tt>).\
</p>\
\
<p>\
The different models used by Augustus were trained on a number of different species-specific\
gene sets, which included 1000-2000 training gene structures. The <tt>--species</tt> option allows\
one to choose the species used for training the models. Different training species were used\
for the <tt>--species</tt> option when generating these predictions for different groups of\
assemblies.\
<table class="stdTbl">\
\	<tr>\
\	\	<td align=center><b>Assembly Group</b></td>\
\	\	<td align=center><b>Training Species</b></td>\
\	</tr>\
\	<tr>\
\	\	<td align=center>Fish</td>\
\	\	<td align=center><tt>zebrafish</tt>\
\	</tr>\
\	<tr>\
\	\	<td align=center>Birds</td>\
\	\	<td align=center><tt>chicken</tt>\
\	</tr>\
\	<tr>\
\	\	<td align=center>Human and all other vertebrates</td>\
\	\	<td align=center><tt>human</tt>\
\	</tr>\
\	<tr>\
\	\	<td align=center>Nematodes</td>\
\	\	<td align=center><tt>caenorhabditis</tt></td>\
\	</tr>\
\	<tr>\
\	\	<td align=center>Drosophila</td>\
\	\	<td align=center><tt>fly</tt></td>\
\	</tr>\
\	<tr>\
\	\	<td align=center><em>A. mellifera</em></td>\
\	\	<td align=center><tt>honeybee1</tt></td>\
\	</tr>\
\	<tr>\
\	\	<td align=center><em>A. gambiae</em></td>\
\	\	<td align=center><tt>culex</tt></td>\
\	</tr>\
\	<tr>\
\	\	<td align=center><em>S. cerevisiae</em></td>\
\	\	<td align=center><tt>saccharomyces</tt></td>\
\	</tr>\
</table>\
<p>\
This table describes which training species was used for a particular group of assemblies.\
When available, the closest related training species was used.\
</p>\
\
<h2>Credits</h2>\
\
Thanks to the\
<a href="https://math-inf.uni-greifswald.de/en/department/about-us/employees/prof-dr-mario-stanke-english/"\
target="_blank">Stanke lab</a>\
for providing the AUGUSTUS program.  The training for the <tt>chicken</tt> version was\
done by Stefanie K&ouml;nig and the training for the\
<tt>human</tt> and <tt>zebrafish</tt> versions was done by Mario Stanke.\
\
<h2>References</h2>\
\
<p>\
Stanke M, Diekhans M, Baertsch R, Haussler D.\
<a href="https://academic.oup.com/bioinformatics/article/24/5/637/202844/Using-native-and-syntenically-mapped-cDNA"\
target="_blank">\
Using native and syntenically mapped cDNA alignments to improve de novo gene finding</a>.\
<em>Bioinformatics</em>. 2008 Mar 1;24(5):637-44.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18218656" target="_blank">18218656</a>\
</p>\
\
<p>\
Stanke M, Waack S.\
<a href="https://academic.oup.com/bioinformatics/article/19/suppl_2/ii215/180603/Gene-prediction-with-a-hidden-Markov-model-and-a"\
target="_blank">\
Gene prediction with a hidden Markov model and a new intron submodel</a>.\
<em>Bioinformatics</em>. 2003 Oct;19 Suppl 2:ii215-25.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14534192" target="_blank">14534192</a>\
</p>\
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type genePred\
visibility hide\

bacEndPairs	BAC End Pairs	bed 6 +	BAC End Pairs	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
Bacterial artificial chromosomes (BACs) are a key part of many large\
scale sequencing projects.  A BAC typically consists of 25 - 350 kb of\
DNA.  During the early phase of a sequencing project, it is common\
to sequence a single read (approximately 500 bases) off each end of\
a large number of BACs.  Later on in the project, these BAC end reads\
can be mapped to the genome sequence.</P>\
<P>\
This track shows these mappings\
in cases where both ends could be mapped.  These BAC end pairs can\
be useful for validating the assembly over relatively long ranges.  In some\
cases, the BACs are useful biological reagents.  This track can also be\
used for determining which BAC contains a given gene, useful information\
for certain wet lab experiments.</P>\
<P>\
A valid pair of BAC end sequences must be\
at least 25 kb but no more than 350 kb away from each other. \
The orientation of the first BAC end sequence must be &quot;+&quot; and\
the orientation of the second BAC end sequence must be &quot;-&quot;.</P>\
<P>\
The scoring scheme used for this annotation assigns 1000 to an alignment \
when the BAC end pair aligns to only one location in the genome (after \
filtering).  When a BAC end pair or clone aligns to multiple locations, the \
score is calculated as 1500/(number of alignments).</P>\
\
<H2>Methods</H2>\
<P>\
BAC end sequences are placed on the assembled sequence using\
Jim Kent's <A HREF="https://genome.cshlp.org/content/12/4/656.abstract"\
TARGET=_blank>blat</A> program.</P>\
\
<H2>Credits</H2>\
<P>\
Additional information about the clone, including how it\
can be obtained, may be found at the \
<A HREF="https://ncbiinsights.ncbi.nlm.nih.gov/2019/05/01/clone-db-retirement/" \
TARGET=_blank>NCBI Clone Registry</A>. To view the registry entry for a \
specific clone, open the details page for the clone and click on its name at \
the top of the page. </P>\
	map	1	exonArrows off\
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wgEncodeCaltechHist	Caltech Histone	bed 3	Histone Modifications by ChIP-seq from ENCODE/Caltech	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
\
<h3>Rationale for the Mouse ENCODE project</h3>\
<p>Our knowledge of the function of genomic DNA sequences comes from three \
basic approaches. Genetics uses changes in behavior or structure of a cell or organism\
in response to changes in DNA sequence to infer function of the altered sequence. \
Biochemical approaches monitor states of histone modification, binding of specific \
transcription factors, accessibility to DNases and other epigenetic features along \
genomic DNA. In general, these are associated with gene activity, but the precise \
relationships remain to be established. The third approach is evolutionary, using \
comparisons among homologous DNA sequences to find segments that are evolving \
more slowly or more rapidly than expected given the local rate of neutral change. These \
are inferred to be under negative or positive selection, respectively, and we interpret \
these as DNA sequences needed for a preserved (negative selection) or adaptive \
(positive selection) function. </p>\
\
<p>The ENCODE project aims to discover all the DNA sequences associated with \
various epigenetic features, with the reasonable expectation that these will also be \
functional (best tested by genetic methods). However, it is not clear how to relate these \
results with those from evolutionary analyses. The mouse ENCODE project aims to \
make this connection explicitly and with a moderate breadth. Assays identical to those \
being used in the ENCODE project are performed in cell types in mouse that are similar \
or homologous to those studied in the human project. Thus, we will be able to discover \
which epigenetic features are conserved between mouse and human, and we can \
examine the extent to which these overlap with the DNA sequences under negative \
selection. The contribution of DNA that with a function preserved in mammals versus \
that with a function in only one species will be discovered. The results will have a \
significant impact on our understanding of the evolution of gene regulation.\
</p>\
\
<h3>Maps of Occupancy by Transcription Factors</h3>\
<p>Genome-wide occupancy maps of transcription factors (TFs) are generated by \
ChIP-seq. A ChIP-Seq experiment combines a chromatin immunoprecipitation (ChIP) experiment that \
enriches genomic DNA for the segments bound by specific proteins (the \
antigens recognized by the antibody) with high-throughput short read \
sequencing of the enriched DNA fragments (Wold & Myers, 2008). Proteins are crosslinked to DNA (usually with formaldehyde), \
chromatin is sheared and immunoprecipitated with the antibody of interest. The immunoprecipitated material is turned into a sequencing library and sequenced. \
The sequencing reads are then aligned to the genome. A control sample consisting of sonicated chromatin that has not been immunoprecipitated or \
immunoprecipitated with a non-specific immunoglobulin is also sequenced. The ChIP and the control datasets are analyzed with a variety of software packages \
to identify regions occupied by the target protein. The sequencing data, alignments and analysis files for these experiments are available for download.</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <A HREF="/goldenPath/help/multiView.html" TARGET=_BLANK>here</A>.\
This track contains the following views:\
</p>\
<dl>\
<dt><i>Peaks</i></dt><dd> Regions of signal enrichment based on processed data. Intensity is represented in \
grayscale, the darker shading shows higher intensity (a solid vertical line\
in the peak region represents the point with the highest signal).</dd>\
\
<dt><i>Signal</i></dt><dd> Density graph (wiggle) of signal enrichment based on\
processed data of all mapped read intensity of the signal is represented as RPM (Read Per Million).</dd>\
\
</dl>\
<p>\
Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
</p>\
<p>\
Chromatin immunoprecipitation followed published methods (Johnson & Mortazavi <em> et al.</em>, 2007) with the exception of certain experiments for which glutaraldehyde was added to the crosslink reaction.\
Information on the antibodies used is available via the metadata  for each subtrack. Libraries were constructed using the Illumina ChIP-seq \
Sample Preparation Kit or using a modified protocol that includes the addition of multiplexing tags to the fragments. \
DNA fragments were repaired to generate blunt ends and a single A nucleotide \
was added to each end. Double-stranded Illumina adaptors or Double-stranded Illumina adaptors with multiplexing tags were ligated to the \
fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between \
150-250 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA \
HS Assay Kit. The DNA library was sequenced on the Illumina GAII and GAIIx\
sequencing systems, and more recently, for multiplexed libraries, several of them were pooled and sequenced on the HiSeq platform. Cluster generation, linearization, \
blocking and sequencing primer reagents were provided in the Illumina Cluster \
Amplification kits. Older libraries were generated using 2 rounds of PCR. Matched input samples were sequenced for each variation of \
fixation conditions and the number of PCR rounds. Reads of 32 bp, 36 bp or 50 bp length were generated.\
</p>\
\
<p>\
Sequencing reads (fastq files) were assigned to the corresponding libraries based on the multiplexing tag for pooled libraries \
(all tags have been removed from reads in the fastq files available for download) or directly processed. Bowtie (Langmead <em>et al.</em>, 2009) was used to map reads \
to the male or female version of the mouse genome (excluding the _random chromosomes in the assembly) depending on the cell line sex. The following parameters were used:\
"-v 2 -k 11 -m 10 -t --best --strata". Aligned reads were converted into rds files using the ERANGE package (Johnson & Mortazavi <em>et al.</em>, 2007) and the findall.py program in \
ERANGE was used to identify enriched regions against the matching input sample. The following settings were used for point-source transcription factors: \
 "--shift learn --ratio 3 --minimum 2 --listPeak --revbackground". For histone modifications, the settings were changed to\
"--notrim --nodirectionality --spacing 100 --ratio 3 --minimum 2 --listPeak --revbackground".\
</p>\
\
<h2>Credits</h2>\
\
<p>\
Cell growth, ChIP, and Illumina library construction were done in the laboratory \
of Barbara Wold, (California Institute of Technology). Sequencing was done at the Millard and Muriel Jacobs Genetics and Genomics Laboratory at the California Institute of Technology, initial HiSeq data was generated at Illumina Inc., Hawyard, CA.\
<br><br>\
<b>Cell growth and ChIP:</b>\
\
Georgi Marinov, Katherine Fisher, Gordon Kwan, Antony Kirilusha, Ali Mortazavi, Gilberto DeSalvo, Brian Williams<br>\
\
<b>Library Construction, Sequencing and Primary Data Handling:</b>\
\
Lorianne Schaeffer, Diane Trout , Igor Antoschechkin (California Institute of Technology), \
Lu Zhang, Gary Schroth (Illumina Inc.)<br>\
\
<b>Data Processing and Submission:</b>\
\
Georgi Marinov, Diane Trout<br>\
<br>\
<b>Contact:</b>\
<a href="mailto:&#119;o&#108;&#100;&#98;&#64;&#99;&#97;&#108;&#116;e&#99;&#104;.\
&#101;d&#117;"target="_BLANK">Barbara Wold</a>, \
<a href="mailto:&#103;&#101;&#111;r&#103;i&#64;&#99;&#97;lt&#101;c&#104;.\
&#101;&#100;&#117;" target="_BLANK">Georgi K. Marinov</a>, \
<a href="mailto:&#100;&#105;a&#110;&#101;&#64;&#99;&#97;&#108;&#116;&#101;&#99;h.\
e&#100;u" target="_BLANK">Diane Trout</a><br>\
</p>\
\
<h2>References</h2>\
\
<p>\
Langmead B, Trapnell C, Pop M, Salzberg SL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174" target="_blank">\
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>.\
<em>Genome Biol</em>. 2009;10(3):R25.\
</p>\
\
<p>\
Johnson DS, Mortazavi A, Myers RM, Wold B.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17540862" target="_blank">\
Genome-wide mapping of in vivo protein-DNA interactions</a>.\
<em>Science</em>. 2007 Jun 8;316(5830):1497-502.\
</p>\
\
<p>\
Wold B, Myers RM.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18165803" target="_blank">\
Sequence census methods for functional genomics</a>.\
<em>Nat Methods</em>. 2008 Jan;5(1):19-21.\
</p>\
\
<h2>Data Release Policy</h2>\
\
<p>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <em>Restricted Until</em> column on the track configuration page and\
the download page.  The full data release policy for ENCODE is available\
<a href="../ENCODE/terms.html" target="_BLANK">here</a>.</p>\
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wgEncodeCaltechRnaSeq	Caltech RNA-seq	bed 3	RNA-seq from ENCODE/Caltech	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<h3>Rationale for the Mouse ENCODE project</h3>\
Our knowledge of the function of genomic DNA sequences comes from three \
basic approaches. Genetics uses changes in behavior or structure of a cell or organism\
in response to changes in DNA sequence to infer function of the altered sequence. \
Biochemical approaches monitor states of histone modification, binding of specific \
transcription factors, accessibility to DNases and other epigenetic features along \
genomic DNA. In general, these are associated with gene activity, but the precise \
relationships remain to be established. The third approach is evolutionary, using \
comparisons among homologous DNA sequences to find segments that are evolving \
more slowly or more rapidly than expected given the local rate of neutral change. These \
are inferred to be under negative or positive selection, respectively, and we interpret \
these as DNA sequences needed for a preserved (negative selection) or adaptive \
(positive selection) function. <p></p>\
\
<p>The ENCODE project aims to discover all the DNA sequences associated with \
various epigenetic features, with the reasonable expectation that these will also be \
functional (best tested by genetic methods). However, it is not clear how to relate these \
results with those from evolutionary analyses. The mouse ENCODE project aims to \
make this connection explicitly and with a moderate breadth. Assays identical to those \
being used in the ENCODE project are performed in cell types in mouse that are similar \
or homologous to those studied in the human project. Thus we will be able to discover \
which epigenetic features are conserved between mouse and human, and we can \
examine the extent to which these overlap with the DNA sequences under negative \
selection. The contribution of DNA with a function preserved in mammals versus \
that with a function in only one species will be discovered. The results will have a \
significant impact on our understanding of the evolution of gene regulation.\
</p>\
\
<H3>Reference transcriptome measurements with RNA-seq</H3>\
RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly (Mortazavi <EM>et al.</EM>, 2008).\
RNA-seq is performed by reverse-transcribing an RNA sample into cDNA, followed by high-throughput DNA sequencing,\
which was done here on the Illumina HiSeq sequencer. The transcriptome measurements shown on these tracks were performed on \
<A target="_BLANK" href="/cgi-bin/hgEncodeVocab?term=longPolyA&type=rnaExtract">polyA selected RNA</A> from \
<A target="_BLANK" href="/cgi-bin/hgEncodeVocab?term=cell&type=localization">total cellular RNA</A>. PolyA-selected RNA was fragmented \
by magnesium-catalyzed hydrolysis and then converted into cDNA by random priming and amplified. Paired-end 2x100 bp reads were obtained from each end of a cDNA fragment. \
Reads were aligned to the mm9 human reference genome using TopHat (Trapnell <em>et al.</em>, 2009), a program specifically designed to align RNA-seq reads and discover splice junctions de novo.\
All sequence and alignments files are available on the <A target="_BLANK" href="/cgi-bin/hgFileUi?db=mm9&g=wgEncodeCaltechRnaSeq">downloads page</A>.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<P>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <A href="/goldenPath/help/multiView.html" target="_BLANK">here</A>.\
The following views are in this track:\
<DL>\
<DT><I>Alignments</I></DT>\
<DD>The Alignments (BAM file) view shows reads aligned to the genome. Alignments are colored by cell type. See the <a href="http://bowtie-bio.sourceforge.net/manual.shtml#sam-bowtie-output" target=_blank>Bowtie Manual</a> (Langmead <em>et al.</em>, 2009)\
for information about the SAM Bowtie output (including other tags) and the \
<a href="https://samtools.github.io/hts-specs/SAMv1.pdf#page=4" target=_blank>SAM Format Specification</a> for information on \
the SAM/BAM file format. </DD></DT>\
<DT><I>Raw Signal</I></DT>\
<DD>Density graph (wiggle) of signal enrichment based on a normalized aligned \
read density (Read Per Million, RPM). The RPM measure assists in visualizing the relative amount of a given transcript across multiple samples. This is used to display all reads in this track.</DD>\
<DT><I>Signal (Unique Reads)</I></DT>\
<DD>Density graph (wiggle) of signal enrichment based on processed data. This is used to display uniquely mapped reads in this track.</DD>\
</DL>\
\
<P>\
<!--echo var="BROWSER_HOST" -->\
Additional views are available on the Downloads page. \
</P>\
\
<H2>Methods</H2>\
\
<H3>Experimental Procedures</H3>\
\
<P> \
Cells were grown according to the approved <a href="/ENCODE/protocols/cell/mouse" target="_BLANK">ENCODE cell culture protocols</a>. \
Cells were lysed in RLT buffer (Qiagen RNEasy kit), and processed on RNEasy midi columns according to the manufacturer's protocol, with the inclusion of the "on-column" DNAse digestion step to remove residual genomic DNA. A quantity of 75 µgs of total RNA was selected twice with oligo-dT beads (Dynal) according to the manufacturer's \
protocol to isolate mRNA from each of the preparations.  A quantity of 100 ngs of mRNA was \
then processed according to the protocol in Mortazavi <EM>et al.</EM> (2008), and prepared for sequencing on the Illumina GAIIx or HiSeq platforms \
 according to the protocol for the ChIP-Seq DNA genomic DNA kit (Illumina). Paired-end libraries were size-selected around 200 bp (fragment length).\
 \
Libraries were sequenced with the Illumina HiSeq according to the manufacturer's recommendations. Paired-end reads of 100 bp length were obtained\
\
<H3>Data Processing and Analysis</H3>\
 \
<P>Reads were mapped to the reference mouse genome (version mm9 with or without the Y chromosome, depending on the sex of the cell line, \
and without the random chromosomes in all cases) using <A href="http://tophat.cbcb.umd.edu/" target="_BLANK">TopHat</A> (version 1.3.1).  TopHat was used with default settings with the exception of specifying an empirically determined mean inner-mate distance and supplying known ENSEMBL version 63 splice junctions.</P>\
\
<H2>Credits</H2>\
\
<P>Wold Group: Brian Williams, Georgi Marinov, Diane Trout, Lorian Schaeffer, Gordon Kwan, Katherine Fisher, Gilberto De Salvo, Ali Mortazavi, Henry Amrhein, Brandon King </P>\
\
<P>\
Contacts: \
<A href="mailto:georgi@caltech.edu">\
Georgi Marinov</A> (data coordination/informatics/experimental),\
<!-- above address is georgi at caltech.edu -->\
<A href="mailto:diane@caltech.edu">\
Diane Trout</A> (informatics) and\
<!-- above address is diane at caltech.edu -->\
<A href="mailto:bawilli_91125@yahoo.com">\
Brian Williams</A> (experimental)\
<!-- above address is bawilli_91125 at yahoo.com -->\
</P>\
\
<H2>References</H2>\
\
<p>\
Langmead B, Trapnell C, Pop M, Salzberg SL.\
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25" target="_blank">\
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>.\
<em>Genome Biol</em>. 2009;10(3):R25.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174" target="_blank">19261174</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996/" target="_blank">PMC2690996</a>\
</p>\
\
<p>\
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.\
<a href="https://www.nature.com/articles/nmeth.1226" target="_blank">\
Mapping and quantifying mammalian transcriptomes by RNA-Seq</a>.\
<em>Nat Methods</em>. 2008 Jul;5(7):621-8.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18516045" target="_blank">18516045</a>\
</p>\
\
<p>\
Trapnell C, Pachter L, Salzberg SL.\
<a href="https://academic.oup.com/bioinformatics/article/25/9/1105/203994" target="_blank">\
TopHat: discovering splice junctions with RNA-Seq</a>.\
<em>Bioinformatics</em>. 2009 May 1;25(9):1105-11.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19289445" target="_blank">19289445</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672628/" target="_blank">PMC2672628</a>\
</p>\
\
<H2> Data Release Policy </H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column, above.  The full data release policy\
for ENCODE is available\
<A href="/ENCODE/terms.html" target="_BLANK">here</A>.</P>\
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wgEncodeCaltechTfbs	Caltech TFBS	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
\
<h3>Rationale for the Mouse ENCODE project</h3>\
<p>Our knowledge of the function of genomic DNA sequences comes from three \
basic approaches. Genetics uses changes in behavior or structure of a cell or organism\
in response to changes in DNA sequence to infer function of the altered sequence. \
Biochemical approaches monitor states of histone modification, binding of specific \
transcription factors, accessibility to DNases and other epigenetic features along \
genomic DNA. In general, these are associated with gene activity, but the precise \
relationships remain to be established. The third approach is evolutionary, using \
comparisons among homologous DNA sequences to find segments that are evolving \
more slowly or more rapidly than expected given the local rate of neutral change. These \
are inferred to be under negative or positive selection, respectively, and we interpret \
these as DNA sequences needed for a preserved (negative selection) or adaptive \
(positive selection) function. </p>\
\
<p>The ENCODE project aims to discover all the DNA sequences associated with \
various epigenetic features, with the reasonable expectation that these will also be \
functional (best tested by genetic methods). However, it is not clear how to relate these \
results with those from evolutionary analyses. The mouse ENCODE project aims to \
make this connection explicitly and with a moderate breadth. Assays identical to those \
being used in the ENCODE project are performed in cell types in mouse that are similar \
or homologous to those studied in the human project. Thus, we will be able to discover \
which epigenetic features are conserved between mouse and human, and we can \
examine the extent to which these overlap with the DNA sequences under negative \
selection. The contribution of DNA that with a function preserved in mammals versus \
that with a function in only one species will be discovered. The results will have a \
significant impact on our understanding of the evolution of gene regulation.\
</p>\
\
<h3>Maps of Occupancy by Transcription Factors</h3>\
Genome-wide occupancy maps of transcription factors (TFs) are generated by \
ChIP-seq. A ChIP-Seq experiment combines a chromatin immunoprecipitation (ChIP) experiment that \
enriches genomic DNA for the segments bound by specific proteins (the \
antigens recognized by the antibody) with high-throughput short read \
sequencing of the enriched DNA fragments (Wold & Myers, 2008). Proteins are crosslinked to DNA (usually with formaldehyde), \
chromatin is sheared and immunoprecipitated with the antibody of interest. The immunoprecipitated material is turned into a sequencing library and sequenced. \
The sequencing reads are then aligned to the genome. A control sample consisting of sonicated chromatin that has not been immunoprecipitated or \
immunoprecipitated with a non-specific immunoglobulin is also sequenced. The ChIP and the control datasets are analyzed with a variety of software packages \
to identify regions occupied by the target protein. The sequencing data, alignments and analysis files for these experiments are available for download. <p></p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <A HREF="/goldenPath/help/multiView.html" TARGET=_BLANK>here</A>.\
This track contains the following views:\
</p>\
<dl>\
<dt><i>Peaks</i></dt><dd> Regions of signal enrichment based on processed data. Intensity is represented in \
grayscale, the darker shading shows higher intensity (a solid vertical line\
in the peak region represents the point with the highest signal).</dd>\
\
<dt><i>Signal</i></dt><dd> Density graph (wiggle) of signal enrichment based on\
processed data of all mapped read intensity of the signal is represented as RPM (Read Per Million).</dd>\
\
</dl>\
<p>\
Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
</p>\
<p>\
Chromatin immunoprecipitation followed published methods (Johnson & Mortazavi <em> et al.</em>, 2007) with the exception of certain experiments for which glutaraldehyde was added to the crosslink reaction.\
Information on the antibodies used is available via the metadata  for each subtrack. Libraries were constructed using the Illumina ChIP-seq \
Sample Preparation Kit or using a modified protocol that includes the addition of multiplexing tags to the fragments. \
DNA fragments were repaired to generate blunt ends and a single A nucleotide \
was added to each end. Double-stranded Illumina adaptors or Double-stranded Illumina adaptors with multiplexing tags were ligated to the \
fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between \
150-250 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA \
HS Assay Kit. The DNA library was sequenced on the Illumina GAII and GAIIx\
sequencing systems, and more recently, for multiplexed libraries, several of them were pooled and sequenced on the HiSeq platform. Cluster generation, linearization, \
blocking and sequencing primer reagents were provided in the Illumina Cluster \
Amplification kits. Older libraries were generated using 2 rounds of PCR. Matched input samples were sequenced for each variation of \
fixation conditions and the number of PCR rounds. Reads of 32 bp, 36 bp or 50 bp length were generated.\
</p>\
\
<p>\
Sequencing reads (fastq files) were assigned to the corresponding libraries based on the multiplexing tag for pooled libraries \
(all tags have been removed from reads in the fastq files available for download) or directly processed. Bowtie (Langmead <em>et al.</em>, 2009) was used to map reads \
to the male or female version of the mouse genome (excluding the _random chromosomes in the assembly) depending on the cell line sex. The following parameters were used:\
"-v 2 -k 11 -m 10 -t --best --strata". Aligned reads were converted into rds files using the ERANGE package (Johnson & Mortazavi <em>et al.</em>, 2007) and the findall.py program in \
ERANGE was used to identify enriched regions against the matching input sample. The following settings were used for point-source transcription factors: \
 "--shift learn --ratio 3 --minimum 2 --listPeak --revbackground". For histone modifications, the settings were changed to\
"--notrim --nodirectionality --spacing 100 --ratio 3 --minimum 2 --listPeak --revbackground".\
</p>\
\
<h2>Credits</h2>\
\
<p>\
Cell growth, ChIP, and Illumina library construction were done in the laboratory \
of Barbara Wold, (California Institute of Technology). Sequencing was done at the Millard and Muriel Jacobs Genetics and Genomics Laboratory at the California Institute of Technology, initial HiSeq data was generated at Illumina Inc., Hawyard, CA.\
<br><br>\
<b>Cell growth and ChIP:</b>\
\
Georgi Marinov, Katherine Fisher, Gordon Kwan, Antony Kirilusha, Ali Mortazavi, Gilberto DeSalvo, Brian Williams<br>\
\
<b>Library Construction, Sequencing and Primary Data Handling:</b>\
\
Lorianne Schaeffer, Diane Trout , Igor Antoschechkin (California Institute of Technology), \
Lu Zhang, Gary Schroth (Illumina Inc.)<br>\
\
<b>Data Processing and Submission:</b>\
\
Georgi Marinov, Diane Trout<br>\
<br>\
<b>Contact:</b>\
<a href="mailto:&#119;o&#108;&#100;&#98;&#64;&#99;&#97;&#108;&#116;e&#99;&#104;.\
&#101;d&#117;"target="_BLANK">Barbara Wold</a>, \
<a href="mailto:&#103;&#101;&#111;r&#103;i&#64;&#99;&#97;lt&#101;c&#104;.\
&#101;&#100;&#117;" target="_BLANK">Georgi K. Marinov</a>, \
<a href="mailto:&#100;&#105;a&#110;&#101;&#64;&#99;&#97;&#108;&#116;&#101;&#99;h.\
e&#100;u" target="_BLANK">Diane Trout</a><br>\
</p>\
\
<h2>References</h2>\
\
<p>\
Langmead B, Trapnell C, Pop M, Salzberg SL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174" target="_blank">\
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>.\
<em>Genome Biol</em>. 2009;10(3):R25.\
</p>\
\
<p>\
Johnson DS, Mortazavi A, Myers RM, Wold B.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17540862" target="_blank">\
Genome-wide mapping of in vivo protein-DNA interactions</a>.\
<em>Science</em>. 2007 Jun 8;316(5830):1497-502.\
</p>\
\
<p>\
Wold B, Myers RM.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18165803" target="_blank">\
Sequence census methods for functional genomics</a>.\
<em>Nat Methods</em>. 2008 Jan;5(1):19-21.\
</p>\
\
<h2>Data Release Policy</h2>\
\
<p>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <em>Restricted Until</em> column on the track configuration page and\
the download page.  The full data release policy for ENCODE is available\
<a href="../ENCODE/terms.html" target="_BLANK">here</a>.</p>\
	regulation	1	compositeTrack on\
controlledVocabulary encode/cv.ra cellType=cell factor=antibody sex=sex control=control treatment=treatment protocol=protocol\
dimensionAchecked CNTRL32B,CNTRL50B,CNTRL36B\
dimensionBchecked rep1\
dimensions dimensionX=treatment dimensionY=factor dimensionA=control dimensionB=rep\
dragAndDrop subTracks\
fileSortOrder cell=Cell_Line antibody=Antibody<BR>Target control=Control treatment=Treatment protocol=Protocol replicate=Replicate view=View dccAccession=UCSC_Accession fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until\
filterComposite dimensionA=multi dimensionB=multi\
group regulation\
longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech\
noInherit on\
priority 0\
shortLabel Caltech TFBS\
sortOrder cellType=+ factor=+ control=+ treatment=+ protocol=+ rep=+ view=+\
subGroup1 view Views Peaks=Peaks Signal=Signal\
subGroup2 cellType Cell_Line C2C12=C2C12\
subGroup3 factor Factor CEBPB=CEBPB CTCF=CTCF E2F4=E2F4 FOSL1SC605=FOSL1_(sc-605) MAX=MAX SC32758=MyoD_(sc-32758) SC12732=Myogenin_(sc-12732) NRSF=NRSF POL2=POL2 POL2S2=Pol2(phosphoS2) SRF=SRF TCF3=TCF3_(SC-349) TCF12=TCF12 USF1=USF-1 INPUT=Input\
subGroup4 sex Sex F=F\
subGroup5 control Control CNTRL32B=Control_32bp CNTRL36B=Control_36bp CNTRL50B=Control_50bp\
subGroup6 treatment Treatment NONE=None E2P24H=EqS_2.0pct_24h E2P60H=EqS_2.0pct_60h E2P5D=EqS_2.0pct_5d E2P7D=EqS_2.0pct_7d\
subGroup7 protocol Protocol PCR1X=PCR1x PCR2X=PCR2x\
subGroup8 rep Rep rep1=1 rep2=2 rep3=3\
track wgEncodeCaltechTfbs\
type bed 3\
visibilityViewDefaults Peaks=pack Signal=full\

ccdsGene	CCDS	genePred	Consensus CDS	0	100	12	120	12	133	187	133	0	0	0			<H2>Description</H2>\
<P>\
This track shows mouse genome high-confidence gene annotations from the\
<A HREF="https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi" TARGET=_blank>Consensus \
Coding Sequence (CCDS) project</A>. This project is a collaborative effort \
to identify a core set of \
mouse protein-coding regions that are consistently annotated and of high \
quality. The long-term goal is to support convergence towards a standard set \
of gene annotations on the mouse genome.\
</P>\
<P>Collaborators include:\
<UL>\
<LI><A HREF="https://www.ebi.ac.uk/" TARGET=_blank>European Bioinformatics \
Institute</A> (EBI)\
<LI><A HREF="https://www.ncbi.nlm.nih.gov" TARGET=_blank>National Center for \
Biotechnology Information</A> (NCBI)\
<LI><A HREF="http://www.cbse.ucsc.edu/" TARGET=_blank>University of \
California, Santa Cruz</A> (UCSC)\
<LI><A HREF="https://www.sanger.ac.uk/" TARGET=_blank>Wellcome Trust Sanger \
Institute</A> (WTSI)\
</UL>\
\
<p>\
For more information on the different gene tracks, see our <a target=_blank \
href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>\
\
<H2>Methods</H2>\
<P>\
CDS annotations of the mouse genome were obtained from two sources:\
<A HREF="https://www.ncbi.nlm.nih.gov/refseq/" TARGET=_blank>NCBI \
RefSeq</A> and a union of the gene annotations from \
<A HREF="http://www.ensembl.org/index.html" TARGET=_blank>Ensembl</A> and \
<A HREF="http://vega.archive.ensembl.org/index.html" TARGET=_blank>Vega</A>, collectively known \
as <EM>Hinxton</EM>.</P>\
<P>\
Genes with identical CDS genomic coordinates in both sets become CCDS \
candidates. The genes undergo a quality evaluation, which must be approved by \
all collaborators. The following criteria are currently used to assess each\
gene: \
<UL>\
<LI> an initiating ATG (Exception: a non-ATG translation start codon is \
annotated if it has sufficient experimental support), a valid stop codon, and \
no in-frame stop codons (Exception: selenoproteins, which contain a TGA codon \
that is known to be translated to a selenocysteine instead of functioning as \
a stop codon) \
<LI> ability to be translated from the genome reference sequence without frameshifts\
<LI> recognizable splicing sites\
<LI> no intersection with putative pseudogene predictions\
<LI> supporting transcripts and protein homology\
<LI> conservation evidence with other species\
</UL></P>\
<P>\
A unique CCDS ID is assigned to the CCDS, which links together all gene \
annotations with the same CDS.  CCDS gene annotations are under continuous\
review, with periodic updates to this track.\
</P>\
\
<H2>Credits</H2>\
<P>\
This track was produced at UCSC from data downloaded from the\
<A HREF="https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi" TARGET=_blank>CCDS project</A> \
web site.\
</P>\
\
<H2>References</H2>\
<p>\
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T <em>et\
al</em>.\
<a href="https://academic.oup.com/nar/article/30/1/38/1332872/The-Ensembl-genome-database-project"\
target="_blank">The Ensembl genome database project</a>.\
<em>Nucleic Acids Res</em>. 2002 Jan 1;30(1):38-41.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11752248" target="_blank">11752248</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99161/" target="_blank">PMC99161</a>\
</p>\
<p>\
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE,\
Ruef BJ <em>et al</em>.\
<a href="https://genome.cshlp.org/content/19/7/1316.long" target="_blank">\
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the\
human and mouse genomes</a>.\
<em>Genome Res</em>. 2009 Jul;19(7):1316-23.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19498102" target="_blank">19498102</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2704439/" target="_blank">PMC2704439</a>\
</p>\
<p>\
Pruitt KD, Tatusova T, Maglott DR.\
<a href="https://academic.oup.com/nar/article/33/suppl_1/D501/2505241/NCBI-Reference-Sequence-\
RefSeq-a-curated-non" target="_blank">\
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts\
and proteins</a>.\
<em>Nucleic Acids Res</em>. 2005 Jan 1;33(Database issue):D501-4.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15608248" target="_blank">15608248</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979/" target="_blank">PMC539979</a>\
</p>\
	genes	1	baseColorDefault genomicCodons\
baseColorUseCds given\
color 12,120,12\
group genes\
longLabel Consensus CDS\
shortLabel CCDS\
track ccdsGene\
type genePred\
visibility hide\

cytoBand	Chromosome Band	bed 4 +	Chromosome Bands Based On Microscopy	0	100	0	0	0	150	50	50	0	0	0			<H2>Description</H2>\
<P>The chromosome band track represents the approximate \
location of bands seen on Giemsa-stained chromosomes.\
</P>\
<H2>Methods</H2>\
<P> Data are derived from the ideogram.gz file downloaded from the NCBI ftp \
site <A HREF = "ftp://ftp.ncbi.nlm.nih.gov/pub/gdp/"\
TARGET = _BLANK>ftp://ftp.ncbi.nlm.nih.gov/pub/gdp/</A>\
(NCBI current version only).\
Band lengths are typically estimated based on FISH or other\
molecular markers interpreted via microscopy. \
\
<H2>Credits</H2>\
<P> We would like to thank NCBI for providing this information.\
Please direct any inquires into the exact method used for each organism\
to NCBI.\
	map	1	altColor 150,50,50\
group map\
longLabel Chromosome Bands Based On Microscopy\
shortLabel Chromosome Band\
track cytoBand\
type bed 4 +\
visibility hide\

cytoBandIdeo	Chromosome Band (Ideogram)	bed 4 +	Chromosome Bands Based on Microscopy (for Ideogram)	1	100	0	0	0	150	50	50	0	0	0				map	1	altColor 150,50,50\
group map\
longLabel Chromosome Bands Based on Microscopy (for Ideogram)\
shortLabel Chromosome Band (Ideogram)\
track cytoBandIdeo\
type bed 4 +\
visibility dense\

wgEncodeCshlLongRnaSeqViewContigs	Contigs	bed 3	Long RNA-seq from ENCODE/Cold Spring Harbor Lab	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Long RNA-seq from ENCODE/Cold Spring Harbor Lab\
parent wgEncodeCshlLongRnaSeq\
shortLabel Contigs\
track wgEncodeCshlLongRnaSeqViewContigs\
view Contigs\
visibility pack\

cpgIslandSuper	CpG Islands	bed 4 +	CpG Islands (Islands < 300 Bases are Light Green)	0	100	0	100	0	128	228	128	0	0	0			<h2>Description</h2>\
\
<p>CpG islands are associated with genes, particularly housekeeping\
genes, in vertebrates.  CpG islands are typically common near\
transcription start sites and may be associated with promoter\
regions.  Normally a C (cytosine) base followed immediately by a \
G (guanine) base (a CpG) is rare in\
vertebrate DNA because the Cs in such an arrangement tend to be\
methylated.  This methylation helps distinguish the newly synthesized\
DNA strand from the parent strand, which aids in the final stages of\
DNA proofreading after duplication.  However, over evolutionary time,\
methylated Cs tend to turn into Ts because of spontaneous\
deamination.  The result is that CpGs are relatively rare unless\
there is selective pressure to keep them or a region is not methylated\
for some other reason, perhaps having to do with the regulation of gene\
expression.  CpG islands are regions where CpGs are present at\
significantly higher levels than is typical for the genome as a whole.</p>\
\
<p>\
The unmasked version of the track displays potential CpG islands\
that exist in repeat regions and would otherwise not be visible\
in the repeat masked version.\
</p>\
\
<p>\
By default, only the masked version of the track is displayed.  To view the\
unmasked version, change the visibility settings in the track controls at\
the top of this page.\
</p>\
\
<h2>Methods</h2>\
\
<p>CpG islands were predicted by searching the sequence one base at a\
time, scoring each dinucleotide (+17 for CG and -1 for others) and\
identifying maximally scoring segments.  Each segment was then\
evaluated for the following criteria:\
\
<ul>\
\	<li>GC content of 50% or greater</li>\
\	<li>length greater than 200 bp</li>\
\	<li>ratio greater than 0.6 of observed number of CG dinucleotides to the expected number on the \
\	basis of the number of Gs and Cs in the segment</li>\
</ul>\
</p>\
<p>\
The entire genome sequence, masking areas included, was\
used for the construction of the  track <em>Unmasked CpG</em>.\
The track <em>CpG Islands</em> is constructed on the sequence after\
all masked sequence is removed.\
</p>\
\
<p>The CpG count is the number of CG dinucleotides in the island.  \
The Percentage CpG is the ratio of CpG nucleotide bases\
(twice the CpG count) to the length.  The ratio of observed to expected \
CpG is calculated according to the formula (cited in \
Gardiner-Garden <em>et al</em>. (1987)):\
\
<pre>    Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)</pre>\
\
where N = length of sequence.</p>\
<p>\
The calculation of the track data is performed by the following command sequence:\
<pre>\
twoBitToFa <em>assembly.2bit</em> stdout | maskOutFa stdin hard stdout \\\
  | cpg_lh /dev/stdin 2&gt; cpg_lh.err \\\
    |  awk '{&dollar;2 = &dollar;2 - 1; width = &dollar;3 - &dollar;2;  printf("%s\\t%d\\t%s\\t%s %s\\t%s\\t%s\\t%0.0f\\t%0.1f\\t%s\\t%s\\n", &dollar;1, &dollar;2, &dollar;3, &dollar;5, &dollar;6, width, &dollar;6, width*&dollar;7*0.01, 100.0*2*&dollar;6/width, &dollar;7, &dollar;9);}' \\\
     | sort -k1,1 -k2,2n &gt; cpgIsland.bed\
</pre>\
The <em>unmasked</em> track data is constructed from\
<em>twoBitToFa -noMask</em> output for the <em>twoBitToFa</em> command.\
</p>\
\
<h2>Data access</h2>\
<p>\
CpG islands and its associated tables can be explored interactively using the\
<a href="../goldenPath/help/api.html" target="_blank">REST API</a>, the\
<a href="/cgi-bin/hgTables" target="_blank">Table Browser</a> or the\
<a href="/cgi-bin/hgIntegrator" target="_blank">Data Integrator</a>.\
All the tables can also be queried directly from our public MySQL\
servers, with more information available on our\
<a target="_blank" href="/goldenPath/help/mysql.html">help page</a> as well as on\
<a target="_blank" href="http://genome.ucsc.edu/blog/tag/mysql/">our blog</a>.</p>\
<p>\
The source for the <em>cpg_lh</em> program can be obtained from\
<a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/tree/master/src/utils/cpgIslandExt/" target=_blank>src/utils/cpgIslandExt/</a>.\
The <em>cpg_lh</em> program binary can be obtained from: <a href="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh" download="cpg_lh">http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/cpg_lh</a> (choose "save file")\
</p>\
\
<h2>Credits</h2>\
\
<p>This track was generated using a modification of a program developed by G. Miklem and L. Hillier \
(unpublished).</p>\
\
<h2>References</h2>\
\
<p>\
Gardiner-Garden M, Frommer M.\
<a href="https://www.sciencedirect.com/science/article/pii/0022283687906899" target="_blank">\
CpG islands in vertebrate genomes</a>.\
<em>J Mol Biol</em>. 1987 Jul 20;196(2):261-82.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/3656447" target="_blank">3656447</a>\
</p>\
	regulation	1	altColor 128,228,128\
color 0,100,0\
group regulation\
html cpgIslandSuper\
longLabel CpG Islands (Islands < 300 Bases are Light Green)\
shortLabel CpG Islands\
superTrack on\
track cpgIslandSuper\
type bed 4 +\

crispr	CRISPR	bed 3	CRISPR/Cas9 Sp. Pyog. target sites	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
\
<p>\
This track shows regions of the genome within 200 bp of transcribed regions and\
DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme\
from <em>S. pyogenes</em> (PAM: NGG).\
CRISPR target sites were annotated with predicted specificity\
(off-target effects) and predicted efficiency (on-target cleavage) by various\
algorithms through the tool <a href="http://crispor.tefor.net/"\
target="_blank">CRISPOR</a>.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
The track &quot;CRISPR Regions&quot; shows the regions of the genome where target\
sites were analyzed, i.e. within 200 bp of transcribed regions as annotated by\
Ensembl transcript models.</p>\
\
<p>\
The track &quot;CRISPR Targets&quot; shows the target sites in these regions.\
The target sequence of the guide is shown with a thick (exon) bar. The PAM\
motif match (NGG) is shown with a thinner bar. Guides\
are colored to reflect both predicted specificity and efficiency. Specificity\
reflects the &quot;uniqueness&quot; of a 20mer sequence in the genome; the less unique a\
sequence is, the more likely it is to cleave other locations of the genome\
(off-target effects). Efficiency is the frequency of cleavage at the target\
site (on-target efficiency).</p>\
\
<p>Shades of gray stand for sites that are hard to target specifically, as the\
20mer is not very unique in the genome:</p>\
<table class="stdTbl" style="width:100%">\
<tr><td style="width:50px; background-color:#969696"></td><td>impossible to target: target site has at least one identical copy in the genome and was not scored</td></tr>\
<tr><td style="width:50px; background-color:#787878"></td><td>hard to target: many similar sequences in the genome that alignment stopped, repeat?</td></tr>\
<tr><td style="width:50px; background-color:#505050"></td><td>hard to target: target site was aligned but results in a low specificity score &lt;= 50 (see below)</td></tr>\
</table>\
\
<p>Colors highlight targets that are specific in the genome (MIT specificity &gt; 50) but have different predicted efficiencies:</p>\
<table class="stdTbl" style="width:100%">\
<tr><td style="width:50px; background-color:#000064"></td><td>unable to calculate Doench/Fusi 2016 efficiency score</td></tr>\
<tr><td style="width:50px; background-color:#FF7070"></td><td>low predicted cleavage: Doench/Fusi 2016 Efficiency percentile &lt;= 30</td></tr>\
<tr><td style="width:50px; background-color:#FFFF00"></td><td>medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile &gt; 30 and &lt; 55</td></tr>\
<tr><td style="width:50px; background-color:#00b300"></td><td>high predicted cleavage: Doench/Fusi 2016 Efficiency &gt; 55</td></tr>\
</table><BR>\
\
<p>\
Mouse-over a target site to show predicted specificity and efficiency scores:<br>\
<ol>\
<li>The MIT Specificity score summarizes all off-targets into a single number from\
0-100. The higher the number, the fewer off-target effects are expected. We\
recommend guides with an MIT specificity &gt; 50.</li>\
<li>The efficiency score tries to predict if a guide leads to rather strong or\
weak cleavage. According to <a href="#References">(Haeussler et al. 2016)</a>, the <a\
href="https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design">Doench\
2016 Efficiency score</a> should be used to select the guide with the highest\
cleavage efficiency when expressing guides from RNA PolIII Promoters such as\
U6. Scores are given as percentiles, e.g. &quot;70%&quot; means that 70% of mammalian\
guides have a score equal or lower than this guide. The raw score number is\
also shown in parentheses after the percentile.</li>\
<li>The <a\
href="https://www.crisprscan.org/">Moreno-Mateos 2015 Efficiency\
score</a> should be used instead of the Doench 2016 score when transcribing the\
guide in vitro with a T7 promoter, e.g. for injections in mouse, zebrafish or\
Xenopus embryos. The Moreno-Mateos score is given in percentiles and the raw value in parentheses, see the note above.</li> </ol>\
</p>\
\
<p>Click onto features to show all scores and predicted off-targets with up to\
four mismatches. The Out-of-Frame score by <a href="#References">Bae et al. 2014</a>\
is correlated with\
the probability that mutations induced by the guide RNA will disrupt the open\
reading frame. The authors recommend out-of-frame scores &gt; 66 to create\
knock-outs with a single guide efficiently.<p>\
\
<p>Off-target sites are sorted by the CFD (Cutting Frequency Determination) \
score (<a href="https://www.nature.com/articles/nbt.3437"\
target="_blank">Doench et al. 2016</a>). \
The higher the CFD score, the more likely there is off-target cleavage at that site. \
Off-targets with a CFD score &lt; 0.023 are not shown on this page, but are availble  when \
following the link to the external CRISPOR tool. \
When compared against experimentally validated off-targets by \
<a href="#References">Haeussler et al. 2016</a>, the large majority of predicted\
off-targets with CFD scores &lt; 0.023 were false-positives.</p>\
\
<h2>Methods</h2>\
\
<h3>Relationship between predictions and experimental data</h3>\
\
<p>\
Like most algorithms, the MIT specificity score is not always a perfect\
predictor of off-target effects. Despite low scores, many tested guides \
caused few and/or weak off-target cleavage when tested with whole-genome assays\
(Figure 2 from <a href="#References">Haeussler\
et al. 2016</a>), as shown below, and the published data contains few data points\
with high specificity scores. Overall though, the assays showed that the higher\
the specificity score, the lower the off-target effects.</p>\
\
<img src="../images/crisprFig_mitScore.png">\
\
<p>Similarly, efficiency scoring is not very accurate: guides with low\
scores can be efficient and vice versa. As a general rule, however, the higher\
the score, the less likely that a guide is very inefficient. The\
following histograms illustrate, for each type of score, how the share of\
inefficient guides drops with increasing efficiency scores:\
</p>\
\
<img src="../images/crisprFig_effScores.png">\
\
<p>When reading this plot, keep in mind that both scores were evaluated on\
their own training data. Especially for the Moreno-Mateos score, the\
results are too optimistic, due to overfitting. When evaluated on independent\
datasets, the correlation of the prediction with other assays was around 25%\
lower, see <a href="#References">Haeussler et al. 2016</a>. At the time of\
writing, there is no independent dataset available yet to determine the\
Moreno-Mateos accuracy for each score percentile range.</p>\
\
<h3>Track methods</h3>\
<p>\
Exons as predicted by Ensembl Gene models were used, extended by 200 basepairs\
on each side, searched for the -NGG motif. Flanking 20mer guide sequences were\
aligned to the genome with BWA and scored with MIT Specificity scores using the\
command-line version of crispor.org.  Non-unique guide sequences were skipped.\
Flanking sequences were extracted from the genome and input for Crispor\
efficiency scoring, available from the <a\
href="http://crispor.tefor.net/downloads/">Crispor downloads page</a>, which\
includes the Doench 2016, Moreno-Mateos 2015 and Bae\
2014 algorithms, among others.\
</p>\
\
<H2>Data Access</H2>\
<p>\
The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>.\
For automated analysis, the genome annotation is stored in a bigBed file that\
can be downloaded from\
<a href="http://hgdownload.soe.ucsc.edu/gbdb/mm9/crispr/" target="_blank">our download server</a>.\
The files for this track are called <tt>crispr.bb</tt> and <tt>crisprDetails.tab</tt> and are located in the <a href="http://hgdownload.soe.ucsc.edu/gbdb/mm9/crispr/">/gbdb/mm9/crispr</a> directory of our downloads server. Individual\
regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>,\
which can be compiled from the source code or downloaded as a precompiled\
binary for your system. Instructions for downloading source code and binaries can be found\
<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool\
can also be used to obtain only features within a given range, e.g. <tt>bigBedToBed\
http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crispr.bb -chrom=chr21\
-start=0 -end=10000000 stdout</tt> </p>\
\
<p>\
The file crisprDetails.tab includes the details of the off-targets. The last\
column of the bigBed file is the offset of the respective line in\
crisprDetails.tab.  E.g. if the last column is 14227033723, then the following\
command will extract the line with the corresponding off-target details:\
<tt>curl -s -r 14227033723-14227043723 http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crisprDetails.tab | head -n1</tt>. The off-target details can currently not be joined with the table\
browser.</p>\
\
<p>\
The file crisprDetails.tab is a tab-separated text file with two fields. The\
first field contains the numbers of off-targets for each mismatch, e.g. "0,0,1,3,49" \
means 0 off-targets at zero mismatches, 1 at two mismatches, 3 at three and 49\
off-targets at four mismatches. The second field is a pipe-separated list of\
semicolon-separated tuples with the genome coordinates and the CFD score. E.g.\
"chr10;123376795+;42|chr5;148353274-;39" describes two off-targets, with the\
first at chr1:123376795 on the positive strand and a CFD score 0.42</p>\
\
<h2>Credits</h2>\
\
<p>\
Track created by Maximilian Haeussler and Hiram Clawson, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU).\
</p>\
<a name="References"></a>\
<h2>References</h2>\
\
<p>\
Haeussler M, Sch&#246;nig K, Eckert H, Eschstruth A, Miann&#233; J, Renaud JB, Schneider-Maunoury S,\
Shkumatava A, Teboul L, Kent J <em>et al</em>.\
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1012-2"\
target="_blank">Evaluation of off-target and on-target scoring algorithms and integration into the\
guide RNA selection tool CRISPOR</a>.\
<em>Genome Biol</em>. 2016 Jul 5;17(1):148.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27380939" target="_blank">27380939</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934014/" target="_blank">PMC4934014</a>\
</p>\
\
<p>\
Bae S, Kweon J, Kim HS, Kim JS.\
<a href="https://www.nature.com/nmeth/journal/v11/n7/full/nmeth.3015.html" target="_blank">\
Microhomology-based choice of Cas9 nuclease target sites</a>.\
<em>Nat Methods</em>. 2014 Jul;11(7):705-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24972169" target="_blank">24972169</a>\
</p>\
\
<p>\
Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C,\
Orchard R <em>et al</em>.\
<a href="https://www.nature.com/articles/nbt.3437" target="_blank">\
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9</a>.\
<em>Nat Biotechnol</em>. 2016 Feb;34(2):184-91.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26780180" target="_blank">26780180</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744125/" target="_blank">PMC4744125</a>\
</p>\
\
<p>\
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O\
<em>et al</em>.\
<a href="https://www.nature.com/nbt/journal/v31/n9/full/nbt.2647.html" target="_blank">\
DNA targeting specificity of RNA-guided Cas9 nucleases</a>.\
<em>Nat Biotechnol</em>. 2013 Sep;31(9):827-32.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23873081" target="_blank">23873081</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3969858/" target="_blank">PMC3969858</a>\
</p>\
\
<p>\
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ.\
<a href="https://www.nature.com/nmeth/journal/v12/n10/full/nmeth.3543.html" target="_blank">\
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo</a>.\
<em>Nat Methods</em>. 2015 Oct;12(10):982-8.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26322839" target="_blank">26322839</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589495/" target="_blank">PMC4589495</a>\
</p>\
	genes	1	group genes\
html crispr\
longLabel CRISPR/Cas9 Sp. Pyog. target sites\
shortLabel CRISPR\
superTrack on\
track crispr\
type bed 3\
visibility hide\

crisprRanges	CRISPR Regions	bed 3	Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 200 bp)	1	100	110	110	110	182	182	182	0	0	0			<h2>Description</h2>\
\
<p>\
This track shows regions of the genome within 200 bp of transcribed regions and\
DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme\
from <em>S. pyogenes</em> (PAM: NGG).\
CRISPR target sites were annotated with predicted specificity\
(off-target effects) and predicted efficiency (on-target cleavage) by various\
algorithms through the tool <a href="http://crispor.tefor.net/"\
target="_blank">CRISPOR</a>.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
The track &quot;CRISPR Regions&quot; shows the regions of the genome where target\
sites were analyzed, i.e. within 200 bp of transcribed regions as annotated by\
Ensembl transcript models.</p>\
\
<p>\
The track &quot;CRISPR Targets&quot; shows the target sites in these regions.\
The target sequence of the guide is shown with a thick (exon) bar. The PAM\
motif match (NGG) is shown with a thinner bar. Guides\
are colored to reflect both predicted specificity and efficiency. Specificity\
reflects the &quot;uniqueness&quot; of a 20mer sequence in the genome; the less unique a\
sequence is, the more likely it is to cleave other locations of the genome\
(off-target effects). Efficiency is the frequency of cleavage at the target\
site (on-target efficiency).</p>\
\
<p>Shades of gray stand for sites that are hard to target specifically, as the\
20mer is not very unique in the genome:</p>\
<table class="stdTbl" style="width:100%">\
<tr><td style="width:50px; background-color:#969696"></td><td>impossible to target: target site has at least one identical copy in the genome and was not scored</td></tr>\
<tr><td style="width:50px; background-color:#787878"></td><td>hard to target: many similar sequences in the genome that alignment stopped, repeat?</td></tr>\
<tr><td style="width:50px; background-color:#505050"></td><td>hard to target: target site was aligned but results in a low specificity score &lt;= 50 (see below)</td></tr>\
</table>\
\
<p>Colors highlight targets that are specific in the genome (MIT specificity &gt; 50) but have different predicted efficiencies:</p>\
<table class="stdTbl" style="width:100%">\
<tr><td style="width:50px; background-color:#000064"></td><td>unable to calculate Doench/Fusi 2016 efficiency score</td></tr>\
<tr><td style="width:50px; background-color:#FF7070"></td><td>low predicted cleavage: Doench/Fusi 2016 Efficiency percentile &lt;= 30</td></tr>\
<tr><td style="width:50px; background-color:#FFFF00"></td><td>medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile &gt; 30 and &lt; 55</td></tr>\
<tr><td style="width:50px; background-color:#00b300"></td><td>high predicted cleavage: Doench/Fusi 2016 Efficiency &gt; 55</td></tr>\
</table><BR>\
\
<p>\
Mouse-over a target site to show predicted specificity and efficiency scores:<br>\
<ol>\
<li>The MIT Specificity score summarizes all off-targets into a single number from\
0-100. The higher the number, the fewer off-target effects are expected. We\
recommend guides with an MIT specificity &gt; 50.</li>\
<li>The efficiency score tries to predict if a guide leads to rather strong or\
weak cleavage. According to <a href="#References">(Haeussler et al. 2016)</a>, the <a\
href="https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design">Doench\
2016 Efficiency score</a> should be used to select the guide with the highest\
cleavage efficiency when expressing guides from RNA PolIII Promoters such as\
U6. Scores are given as percentiles, e.g. &quot;70%&quot; means that 70% of mammalian\
guides have a score equal or lower than this guide. The raw score number is\
also shown in parentheses after the percentile.</li>\
<li>The <a\
href="https://www.crisprscan.org/">Moreno-Mateos 2015 Efficiency\
score</a> should be used instead of the Doench 2016 score when transcribing the\
guide in vitro with a T7 promoter, e.g. for injections in mouse, zebrafish or\
Xenopus embryos. The Moreno-Mateos score is given in percentiles and the raw value in parentheses, see the note above.</li> </ol>\
</p>\
\
<p>Click onto features to show all scores and predicted off-targets with up to\
four mismatches. The Out-of-Frame score by <a href="#References">Bae et al. 2014</a>\
is correlated with\
the probability that mutations induced by the guide RNA will disrupt the open\
reading frame. The authors recommend out-of-frame scores &gt; 66 to create\
knock-outs with a single guide efficiently.<p>\
\
<p>Off-target sites are sorted by the CFD (Cutting Frequency Determination) \
score (<a href="https://www.nature.com/articles/nbt.3437"\
target="_blank">Doench et al. 2016</a>). \
The higher the CFD score, the more likely there is off-target cleavage at that site. \
Off-targets with a CFD score &lt; 0.023 are not shown on this page, but are availble  when \
following the link to the external CRISPOR tool. \
When compared against experimentally validated off-targets by \
<a href="#References">Haeussler et al. 2016</a>, the large majority of predicted\
off-targets with CFD scores &lt; 0.023 were false-positives.</p>\
\
<h2>Methods</h2>\
\
<h3>Relationship between predictions and experimental data</h3>\
\
<p>\
Like most algorithms, the MIT specificity score is not always a perfect\
predictor of off-target effects. Despite low scores, many tested guides \
caused few and/or weak off-target cleavage when tested with whole-genome assays\
(Figure 2 from <a href="#References">Haeussler\
et al. 2016</a>), as shown below, and the published data contains few data points\
with high specificity scores. Overall though, the assays showed that the higher\
the specificity score, the lower the off-target effects.</p>\
\
<img src="../images/crisprFig_mitScore.png">\
\
<p>Similarly, efficiency scoring is not very accurate: guides with low\
scores can be efficient and vice versa. As a general rule, however, the higher\
the score, the less likely that a guide is very inefficient. The\
following histograms illustrate, for each type of score, how the share of\
inefficient guides drops with increasing efficiency scores:\
</p>\
\
<img src="../images/crisprFig_effScores.png">\
\
<p>When reading this plot, keep in mind that both scores were evaluated on\
their own training data. Especially for the Moreno-Mateos score, the\
results are too optimistic, due to overfitting. When evaluated on independent\
datasets, the correlation of the prediction with other assays was around 25%\
lower, see <a href="#References">Haeussler et al. 2016</a>. At the time of\
writing, there is no independent dataset available yet to determine the\
Moreno-Mateos accuracy for each score percentile range.</p>\
\
<h3>Track methods</h3>\
<p>\
Exons as predicted by Ensembl Gene models were used, extended by 200 basepairs\
on each side, searched for the -NGG motif. Flanking 20mer guide sequences were\
aligned to the genome with BWA and scored with MIT Specificity scores using the\
command-line version of crispor.org.  Non-unique guide sequences were skipped.\
Flanking sequences were extracted from the genome and input for Crispor\
efficiency scoring, available from the <a\
href="http://crispor.tefor.net/downloads/">Crispor downloads page</a>, which\
includes the Doench 2016, Moreno-Mateos 2015 and Bae\
2014 algorithms, among others.\
</p>\
\
<H2>Data Access</H2>\
<p>\
The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>.\
For automated analysis, the genome annotation is stored in a bigBed file that\
can be downloaded from\
<a href="http://hgdownload.soe.ucsc.edu/gbdb/mm9/crisprRanges/" target="_blank">our download server</a>.\
The files for this track are called <tt>crispr.bb</tt> and <tt>crisprDetails.tab</tt> and are located in the <a href="http://hgdownload.soe.ucsc.edu/gbdb/mm9/crispr/">/gbdb/mm9/crispr</a> directory of our downloads server. Individual\
regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>,\
which can be compiled from the source code or downloaded as a precompiled\
binary for your system. Instructions for downloading source code and binaries can be found\
<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool\
can also be used to obtain only features within a given range, e.g. <tt>bigBedToBed\
http://hgdownload.soe.ucsc.edu/gbdb/hg19/crisprRanges/crispr.bb -chrom=chr21\
-start=0 -end=10000000 stdout</tt> </p>\
\
<p>\
The file crisprDetails.tab includes the details of the off-targets. The last\
column of the bigBed file is the offset of the respective line in\
crisprDetails.tab.  E.g. if the last column is 14227033723, then the following\
command will extract the line with the corresponding off-target details:\
<tt>curl -s -r 14227033723-14227043723 http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crisprDetails.tab | head -n1</tt>. The off-target details can currently not be joined with the table\
browser.</p>\
\
<p>\
The file crisprDetails.tab is a tab-separated text file with two fields. The\
first field contains the numbers of off-targets for each mismatch, e.g. "0,0,1,3,49" \
means 0 off-targets at zero mismatches, 1 at two mismatches, 3 at three and 49\
off-targets at four mismatches. The second field is a pipe-separated list of\
semicolon-separated tuples with the genome coordinates and the CFD score. E.g.\
"chr10;123376795+;42|chr5;148353274-;39" describes two off-targets, with the\
first at chr1:123376795 on the positive strand and a CFD score 0.42</p>\
\
<h2>Credits</h2>\
\
<p>\
Track created by Maximilian Haeussler and Hiram Clawson, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU).\
</p>\
<a name="References"></a>\
<h2>References</h2>\
\
<p>\
Haeussler M, Sch&#246;nig K, Eckert H, Eschstruth A, Miann&#233; J, Renaud JB, Schneider-Maunoury S,\
Shkumatava A, Teboul L, Kent J <em>et al</em>.\
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1012-2"\
target="_blank">Evaluation of off-target and on-target scoring algorithms and integration into the\
guide RNA selection tool CRISPOR</a>.\
<em>Genome Biol</em>. 2016 Jul 5;17(1):148.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27380939" target="_blank">27380939</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934014/" target="_blank">PMC4934014</a>\
</p>\
\
<p>\
Bae S, Kweon J, Kim HS, Kim JS.\
<a href="https://www.nature.com/nmeth/journal/v11/n7/full/nmeth.3015.html" target="_blank">\
Microhomology-based choice of Cas9 nuclease target sites</a>.\
<em>Nat Methods</em>. 2014 Jul;11(7):705-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24972169" target="_blank">24972169</a>\
</p>\
\
<p>\
Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C,\
Orchard R <em>et al</em>.\
<a href="https://www.nature.com/articles/nbt.3437" target="_blank">\
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9</a>.\
<em>Nat Biotechnol</em>. 2016 Feb;34(2):184-91.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26780180" target="_blank">26780180</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744125/" target="_blank">PMC4744125</a>\
</p>\
\
<p>\
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O\
<em>et al</em>.\
<a href="https://www.nature.com/nbt/journal/v31/n9/full/nbt.2647.html" target="_blank">\
DNA targeting specificity of RNA-guided Cas9 nucleases</a>.\
<em>Nat Biotechnol</em>. 2013 Sep;31(9):827-32.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23873081" target="_blank">23873081</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3969858/" target="_blank">PMC3969858</a>\
</p>\
\
<p>\
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ.\
<a href="https://www.nature.com/nmeth/journal/v12/n10/full/nmeth.3543.html" target="_blank">\
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo</a>.\
<em>Nat Methods</em>. 2015 Oct;12(10):982-8.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26322839" target="_blank">26322839</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589495/" target="_blank">PMC4589495</a>\
</p>\
	genes	1	color 110,110,110\
html crispr\
longLabel Genome regions processed to find CRISPR/Cas9 target sites (exons +/- 200 bp)\
parent crispr\
shortLabel CRISPR Regions\
track crisprRanges\
type bed 3\
visibility dense\

crisprTargets	CRISPR Targets	bigBed 9 +	CRISPR/Cas9 -NGG Targets	1	100	0	0	0	127	127	127	0	0	0		http://crispor.tefor.net/crispor.py?org=$D&pos=$S:${&pam=NGG	<h2>Description</h2>\
\
<p>\
This track shows regions of the genome within 200 bp of transcribed regions and\
DNA sequences targetable by CRISPR RNA guides using the Cas9 enzyme\
from <em>S. pyogenes</em> (PAM: NGG).\
CRISPR target sites were annotated with predicted specificity\
(off-target effects) and predicted efficiency (on-target cleavage) by various\
algorithms through the tool <a href="http://crispor.tefor.net/"\
target="_blank">CRISPOR</a>.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
The track &quot;CRISPR Regions&quot; shows the regions of the genome where target\
sites were analyzed, i.e. within 200 bp of transcribed regions as annotated by\
Ensembl transcript models.</p>\
\
<p>\
The track &quot;CRISPR Targets&quot; shows the target sites in these regions.\
The target sequence of the guide is shown with a thick (exon) bar. The PAM\
motif match (NGG) is shown with a thinner bar. Guides\
are colored to reflect both predicted specificity and efficiency. Specificity\
reflects the &quot;uniqueness&quot; of a 20mer sequence in the genome; the less unique a\
sequence is, the more likely it is to cleave other locations of the genome\
(off-target effects). Efficiency is the frequency of cleavage at the target\
site (on-target efficiency).</p>\
\
<p>Shades of gray stand for sites that are hard to target specifically, as the\
20mer is not very unique in the genome:</p>\
<table class="stdTbl" style="width:100%">\
<tr><td style="width:50px; background-color:#969696"></td><td>impossible to target: target site has at least one identical copy in the genome and was not scored</td></tr>\
<tr><td style="width:50px; background-color:#787878"></td><td>hard to target: many similar sequences in the genome that alignment stopped, repeat?</td></tr>\
<tr><td style="width:50px; background-color:#505050"></td><td>hard to target: target site was aligned but results in a low specificity score &lt;= 50 (see below)</td></tr>\
</table>\
\
<p>Colors highlight targets that are specific in the genome (MIT specificity &gt; 50) but have different predicted efficiencies:</p>\
<table class="stdTbl" style="width:100%">\
<tr><td style="width:50px; background-color:#000064"></td><td>unable to calculate Doench/Fusi 2016 efficiency score</td></tr>\
<tr><td style="width:50px; background-color:#FF7070"></td><td>low predicted cleavage: Doench/Fusi 2016 Efficiency percentile &lt;= 30</td></tr>\
<tr><td style="width:50px; background-color:#FFFF00"></td><td>medium predicted cleavage: Doench/Fusi 2016 Efficiency percentile &gt; 30 and &lt; 55</td></tr>\
<tr><td style="width:50px; background-color:#00b300"></td><td>high predicted cleavage: Doench/Fusi 2016 Efficiency &gt; 55</td></tr>\
</table><BR>\
\
<p>\
Mouse-over a target site to show predicted specificity and efficiency scores:<br>\
<ol>\
<li>The MIT Specificity score summarizes all off-targets into a single number from\
0-100. The higher the number, the fewer off-target effects are expected. We\
recommend guides with an MIT specificity &gt; 50.</li>\
<li>The efficiency score tries to predict if a guide leads to rather strong or\
weak cleavage. According to <a href="#References">(Haeussler et al. 2016)</a>, the <a\
href="https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design">Doench\
2016 Efficiency score</a> should be used to select the guide with the highest\
cleavage efficiency when expressing guides from RNA PolIII Promoters such as\
U6. Scores are given as percentiles, e.g. &quot;70%&quot; means that 70% of mammalian\
guides have a score equal or lower than this guide. The raw score number is\
also shown in parentheses after the percentile.</li>\
<li>The <a\
href="https://www.crisprscan.org/">Moreno-Mateos 2015 Efficiency\
score</a> should be used instead of the Doench 2016 score when transcribing the\
guide in vitro with a T7 promoter, e.g. for injections in mouse, zebrafish or\
Xenopus embryos. The Moreno-Mateos score is given in percentiles and the raw value in parentheses, see the note above.</li> </ol>\
</p>\
\
<p>Click onto features to show all scores and predicted off-targets with up to\
four mismatches. The Out-of-Frame score by <a href="#References">Bae et al. 2014</a>\
is correlated with\
the probability that mutations induced by the guide RNA will disrupt the open\
reading frame. The authors recommend out-of-frame scores &gt; 66 to create\
knock-outs with a single guide efficiently.<p>\
\
<p>Off-target sites are sorted by the CFD (Cutting Frequency Determination) \
score (<a href="https://www.nature.com/articles/nbt.3437"\
target="_blank">Doench et al. 2016</a>). \
The higher the CFD score, the more likely there is off-target cleavage at that site. \
Off-targets with a CFD score &lt; 0.023 are not shown on this page, but are availble  when \
following the link to the external CRISPOR tool. \
When compared against experimentally validated off-targets by \
<a href="#References">Haeussler et al. 2016</a>, the large majority of predicted\
off-targets with CFD scores &lt; 0.023 were false-positives.</p>\
\
<h2>Methods</h2>\
\
<h3>Relationship between predictions and experimental data</h3>\
\
<p>\
Like most algorithms, the MIT specificity score is not always a perfect\
predictor of off-target effects. Despite low scores, many tested guides \
caused few and/or weak off-target cleavage when tested with whole-genome assays\
(Figure 2 from <a href="#References">Haeussler\
et al. 2016</a>), as shown below, and the published data contains few data points\
with high specificity scores. Overall though, the assays showed that the higher\
the specificity score, the lower the off-target effects.</p>\
\
<img src="../images/crisprFig_mitScore.png">\
\
<p>Similarly, efficiency scoring is not very accurate: guides with low\
scores can be efficient and vice versa. As a general rule, however, the higher\
the score, the less likely that a guide is very inefficient. The\
following histograms illustrate, for each type of score, how the share of\
inefficient guides drops with increasing efficiency scores:\
</p>\
\
<img src="../images/crisprFig_effScores.png">\
\
<p>When reading this plot, keep in mind that both scores were evaluated on\
their own training data. Especially for the Moreno-Mateos score, the\
results are too optimistic, due to overfitting. When evaluated on independent\
datasets, the correlation of the prediction with other assays was around 25%\
lower, see <a href="#References">Haeussler et al. 2016</a>. At the time of\
writing, there is no independent dataset available yet to determine the\
Moreno-Mateos accuracy for each score percentile range.</p>\
\
<h3>Track methods</h3>\
<p>\
Exons as predicted by Ensembl Gene models were used, extended by 200 basepairs\
on each side, searched for the -NGG motif. Flanking 20mer guide sequences were\
aligned to the genome with BWA and scored with MIT Specificity scores using the\
command-line version of crispor.org.  Non-unique guide sequences were skipped.\
Flanking sequences were extracted from the genome and input for Crispor\
efficiency scoring, available from the <a\
href="http://crispor.tefor.net/downloads/">Crispor downloads page</a>, which\
includes the Doench 2016, Moreno-Mateos 2015 and Bae\
2014 algorithms, among others.\
</p>\
\
<H2>Data Access</H2>\
<p>\
The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>.\
For automated analysis, the genome annotation is stored in a bigBed file that\
can be downloaded from\
<a href="http://hgdownload.soe.ucsc.edu/gbdb/mm9/crisprTargets/" target="_blank">our download server</a>.\
The files for this track are called <tt>crispr.bb</tt> and <tt>crisprDetails.tab</tt> and are located in the <a href="http://hgdownload.soe.ucsc.edu/gbdb/mm9/crispr/">/gbdb/mm9/crispr</a> directory of our downloads server. Individual\
regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>,\
which can be compiled from the source code or downloaded as a precompiled\
binary for your system. Instructions for downloading source code and binaries can be found\
<a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool\
can also be used to obtain only features within a given range, e.g. <tt>bigBedToBed\
http://hgdownload.soe.ucsc.edu/gbdb/hg19/crisprTargets/crispr.bb -chrom=chr21\
-start=0 -end=10000000 stdout</tt> </p>\
\
<p>\
The file crisprDetails.tab includes the details of the off-targets. The last\
column of the bigBed file is the offset of the respective line in\
crisprDetails.tab.  E.g. if the last column is 14227033723, then the following\
command will extract the line with the corresponding off-target details:\
<tt>curl -s -r 14227033723-14227043723 http://hgdownload.soe.ucsc.edu/gbdb/hg19/crispr/crisprDetails.tab | head -n1</tt>. The off-target details can currently not be joined with the table\
browser.</p>\
\
<p>\
The file crisprDetails.tab is a tab-separated text file with two fields. The\
first field contains the numbers of off-targets for each mismatch, e.g. "0,0,1,3,49" \
means 0 off-targets at zero mismatches, 1 at two mismatches, 3 at three and 49\
off-targets at four mismatches. The second field is a pipe-separated list of\
semicolon-separated tuples with the genome coordinates and the CFD score. E.g.\
"chr10;123376795+;42|chr5;148353274-;39" describes two off-targets, with the\
first at chr1:123376795 on the positive strand and a CFD score 0.42</p>\
\
<h2>Credits</h2>\
\
<p>\
Track created by Maximilian Haeussler and Hiram Clawson, with helpful input from Jean-Paul Concordet (MNHN Paris) and Alberto Stolfi (NYU).\
</p>\
<a name="References"></a>\
<h2>References</h2>\
\
<p>\
Haeussler M, Sch&#246;nig K, Eckert H, Eschstruth A, Miann&#233; J, Renaud JB, Schneider-Maunoury S,\
Shkumatava A, Teboul L, Kent J <em>et al</em>.\
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1012-2"\
target="_blank">Evaluation of off-target and on-target scoring algorithms and integration into the\
guide RNA selection tool CRISPOR</a>.\
<em>Genome Biol</em>. 2016 Jul 5;17(1):148.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27380939" target="_blank">27380939</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934014/" target="_blank">PMC4934014</a>\
</p>\
\
<p>\
Bae S, Kweon J, Kim HS, Kim JS.\
<a href="https://www.nature.com/nmeth/journal/v11/n7/full/nmeth.3015.html" target="_blank">\
Microhomology-based choice of Cas9 nuclease target sites</a>.\
<em>Nat Methods</em>. 2014 Jul;11(7):705-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24972169" target="_blank">24972169</a>\
</p>\
\
<p>\
Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, Smith I, Tothova Z, Wilen C,\
Orchard R <em>et al</em>.\
<a href="https://www.nature.com/articles/nbt.3437" target="_blank">\
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9</a>.\
<em>Nat Biotechnol</em>. 2016 Feb;34(2):184-91.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26780180" target="_blank">26780180</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744125/" target="_blank">PMC4744125</a>\
</p>\
\
<p>\
Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O\
<em>et al</em>.\
<a href="https://www.nature.com/nbt/journal/v31/n9/full/nbt.2647.html" target="_blank">\
DNA targeting specificity of RNA-guided Cas9 nucleases</a>.\
<em>Nat Biotechnol</em>. 2013 Sep;31(9):827-32.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23873081" target="_blank">23873081</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3969858/" target="_blank">PMC3969858</a>\
</p>\
\
<p>\
Moreno-Mateos MA, Vejnar CE, Beaudoin JD, Fernandez JP, Mis EK, Khokha MK, Giraldez AJ.\
<a href="https://www.nature.com/nmeth/journal/v12/n10/full/nmeth.3543.html" target="_blank">\
CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo</a>.\
<em>Nat Methods</em>. 2015 Oct;12(10):982-8.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26322839" target="_blank">26322839</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4589495/" target="_blank">PMC4589495</a>\
</p>\
	genes	1	detailsTabUrls _offset=/gbdb/$db/crispr/crisprDetails.tab\
html crispr\
itemRgb on\
longLabel CRISPR/Cas9 -NGG Targets\
mouseOverField _mouseOver\
parent crispr\
scoreLabel MIT Guide Specificity Score\
shortLabel CRISPR Targets\
track crisprTargets\
type bigBed 9 +\
url http://crispor.tefor.net/crispor.py?org=$D&pos=$S:${&pam=NGG\
urlLabel Click here to show this guide on Crispor.org, with expression oligos, validation primers and more\
visibility dense\

wgEncodeCshlLongRnaSeq	CSHL Long RNA-seq	bed 3	Long RNA-seq from ENCODE/Cold Spring Harbor Lab	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<p>\
These tracks were generated by the ENCODE Consortium. They contain information \
about mouse RNAs greater than 200 nucleotides in length obtained as short \
reads off the Illumina platform. Data are available from biological replicates. \
</p>\
\
<h2>Display Conventions and Configuration</h2>\
<P>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are\
<a href="/goldenPath/help/multiView.html" target="_blank">here</a>.</P>\
\
<p>To show only selected subtracks, uncheck the boxes next to the tracks that\
you wish to hide.</p>\
\
<p>Color differences among the views are arbitrary. They provide a\
visual cue for\
distinguishing between the different cell types and compartments.</p>\
\
<dl>\
<dt><i>Contigs</i>\
</dt><dd>The Contigs represent blocks of overlapping mapped reads from the pooled biological replicates.\
</dd><dt><i>Raw Signals</i>\
</dt><dd>The Plus Raw Signal and Minus Raw Signal views show the density of mapped reads on the plus and minus strands (wiggle format), respectively.\
</dd>\
<dt><i>Alignments</i>\
</dt><dd>The Alignments view shows individual reads mapped from biological replicates to the genome and indicates where\
bases may mismatch. Every mapped read is displayed, i.e. uncollapsed.  The alignment file follows the standard SAM format of Bowtie output. See the <a href="http://bowtie-bio.sourceforge.net/manual.shtml#sam-bowtie-output" target=_blank>Bowtie Manual</a> for more information about the SAM Bowtie output (including other tags) and the <a href="http://samtools.github.io/hts-specs/SAMv1.pdf#page=4" target=_blank>SAM Format Specification</a> for more information on the SAM/BAM file format. \
</dd>\
<dt><i>Splice Junctions</i>\
</dt><dd>Subset of aligned reads that cross splice junctions. Specific column specifications can be found in the <A TARGET=_BLANK HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/supplemental/">supplemental directory</A>.\
</dd>\
</dl>\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
\
<P>\
<!--echo var="BROWSER_HOST" -->\
Additional <A TARGET=_BLANK HREF="../cgi-bin/hgEncodeVocab?tag=FASTQRD1,FASTQRD2,SPKNS,TRANSDENOVO">views</A> are available on the Downloads page. \
</P>\
\
<H2>Methods</H2>\
\
<H3>Tissue Samples</H3>\
<P> Individual tissues were harvested from mouse strain C57BL/6J at different timepoints\
according to <a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE\
cell culture protocols</A>. \
Whenever possible, biological replicates were obtained from littermates.\
</P>\
\
<H3>Library Preparation</H3>\
<P>The published \
<A TARGET=_BLANK HREF="https://www.ncbi.nlm.nih.gov/pubmed/19620212">\
cDNA sequencing protocol</A> was used.  This protocol generates directional libraries\
and reports the transcripts' strand of origin.  Exogenous RNA spike-ins\
were added to each endogenous RNA isolate and carried\
through library construction and sequencing.  \
The spike-in sequence and the concentrations are available for download\
in the <A TARGET=_BLANK HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/supplemental/">supplemental directory</A>.\
</P>\
\
<H3>Sequencing and Mapping</H3>\
<P>The libraries were sequenced on the Illumina platform (either GAIIx or\
Hi-Seq) in mate-pair fashion (either pair-end 76 or pair-end 101) to an average depth of 100 million\
mate-pairs. \
The data were mapped against mm9 using Spliced Transcript Alignment\
and Reconstruction (STAR) written by Alex Dobin (CSHL).  More\
information about STAR, including the parameters used for these data,\
is available from the\
<A TARGET=_BLANK\
HREF="http://gingeraslab.cshl.edu/STAR/">Gingeras lab</A>.\
</P>\
\
<P>\
For each experiment, there are additional\
<a target="_BLANK" href="../cgi-bin/hgEncodeVocab?tag=EXONSDENOVO,EXONENSV65,GENEDENO,GENENSV65,TRANSDENOVO,TRANSENSV65">element data views</a>\
data files available for <a target="_BLANK" href="../cgi-bin/hgFileUi?db=mm9&g=wgEncodeCshlLongRnaSeq">download</a>.\
These elements were assessed for reproducibility using a nonparametric\
irreproducible detection (IDR) rate script.  The IDR values for each element\
are included in the files for end-users to use as a threshold. An IDR value of 0.1 means\
that the probability of detecting that element in a third experiment equivalent\
in depth to the sum of the bioreplicates is 90&#37;.  In addition,\
expression values for annotated genes, transcripts and exons were computed. Further explanation of these\
files is available for download in the\
<A TARGET=_BLANK HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeCshlLongRnaSeq/supplemental/">supplemental directory</A>.\
</P>\
\
\
<H2>Verification</H2>\
<P>\
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated \
for annotated exons and Spearman correlation coefficients were computed.   \
In general, Rho values are greater than 0.90 between biological replicates.   \
</P>\
\
<H2>Release Notes</H2>\
\
<P>\
This is release 3 (Sept 2012) of this track. It adds data for bladder, cerebellum, CNS, cortex, frontal lobe, limb, liver, placenta, and whole brain. The samples for CNS, liver, limb and whole brain vary over age (developmental stage). \
This release also contains replacement BAM files for the previous ones had the second read reverse complemented.\
</P>\
\
<H2>Credits</H2>\
<P>These data were generated and analyzed by the transcriptome group at\
Cold Spring Harbor Laboratories and the Center for Genomic\
Regulation (CRG in Barcelona), who are participants in the ENCODE Transcriptome Group.\
</P>\
<b>Contacts:</b>\
<A HREF="mailto:&#100;a&#118;&#105;s&#99;&#64;&#99;sh&#108;.&#101;&#100;&#117;">Carrie Davis</A> (experimental),\
<!-- above address is davisc at cshl.edu -->\
<A HREF="mailto:&#114;&#103;&#117;i&#103;o&#64;&#105;&#109;&#105;m.e&#115;">Roderic Guigo</A> and lab (data processing),\
<!-- above address is rguigo at imim.es -->\
<A HREF="mailto:&#103;&#105;&#110;&#103;e&#114;a&#115;&#64;&#99;&#115;&#104;&#108;.&#101;d&#117;">Tom Gingeras</A> (primary investigator)\
<!--above address is gingeras at cshl.edu -->\
\
</P>\
\
<H2>References</H2>\
<p>\
Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B.\
<a href="https://genome.cshlp.org/content/21/9/1543.long" target="_blank">\
Synthetic spike-in standards for RNA-seq experiments</a>.\
<em>Genome Res</em>. 2011 Sep;21(9):1543-51.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21816910" target="_blank">21816910</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166838/" target="_blank">PMC3166838</a>\
</p>\
\
<p>\
Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A.\
<a href="https://academic.oup.com/nar/article/37/18/e123/1085684" target="_blank">\
Transcriptome analysis by strand-specific sequencing of complementary DNA</a>.\
<em>Nucleic Acids Res</em>. 2009 Oct;37(18):e123.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19620212" target="_blank">19620212</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764448/" target="_blank">PMC2764448</a>\
</p>\
\
<H2> Data Release Policy </H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column, above.  The full data release policy\
for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
	regulation	1	compositeTrack on\
controlledVocabulary encode/cv.ra cellType=cell rnaExtract=rnaExtract age=age\
dimensions dimensionY=rep dimensionX=cellType dimensionA=age\
dragAndDrop subTracks\
fileSortOrder cell=Cell_Line replicate=Replicate view=View bioRep=Cross_Lab<BR>BioReplicate labExpId=Lab<BR>Exp_ID dccAccession=UCSC_Accession geoSampleAccession=GEO_Accession fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until\
group regulation\
html wgEncodeCshlLongRnaSeq.release3\
longLabel Long RNA-seq from ENCODE/Cold Spring Harbor Lab\
noInherit on\
priority 0\
shortLabel CSHL Long RNA-seq\
sortOrder cellType=+ age=+ rep=+ view=+\
subGroup1 view Views Contigs=Contigs PlusRawSignal=Plus_Raw_Signal MinusRawSignal=Minus_Raw_Signal SJunctions=Splice_Junctions Alignments=Alignments\
subGroup2 cellType Cell_Line ADRENAL=Adrenal BLADDER=Bladder CBELLUM=Cerebellum CNS=CNS COLON=Colon CORTEX=Cortex DUOD=Duodenum FLOBE=Frontal_Lobe GFAT=Genital_Fat_Pad HEART=Heart KIDNEY=Kidney LGINT=Large_Intestine LIMB=Limb LIVER=Liver LUNG=Lung MAMG=Mammary_Gland OVARY=Ovary PLAC=Placenta SMINT=Small_Intestine SPLEEN=Spleen STOM=Stomach SUFAT=Subcutaneous_Fat_Pad TESTIS=Testis THYMUS=Thymus WBRAIN=Whole_Brain\
subGroup3 age Age ADULT8WKS=Adult_8_wks E11HALF=Embryonic_11.5_days E14=Embryonic_14_days E14HALF=Embryonic_14.5_days E18=Embryonic_18_days\
subGroup4 rep Rep rep1=1 rep2=2 repP=Pooled\
track wgEncodeCshlLongRnaSeq\
type bed 3\

exoniphy	Exoniphy	genePred	Exoniphy Mouse/Rat/Human/Dog	0	100	173	17	162	214	136	208	0	0	0			<H2>Description</H2>\
<P>\
The exoniphy program identifies evolutionarily conserved protein-coding\
exons in a multiple alignment using a phylogenetic hidden Markov\
model (phylo-HMM), a statistical model that simultaneously\
describes exon structure and exon evolution.  This track shows exoniphy\
predictions for the human Mar. 2006 (hg18), mouse Feb. 2006 (mm8), rat\
Nov. 2004 (rn4), and dog May 2005 (canFam2) genomes, as aligned by the\
multiz program.  For this track, only alignments on the &quot;syntenic net&quot;\
between human and each other species were considered. \
</P>\
<P>\
The predictions for mouse Feb. 2006 (mm8) were lifted to\
the mouse Jul. 2007 (mm9) genome.\
</P>\
\
<H2>Methods</H2>\
<P>\
For a description of exoniphy, see Siepel <em>et al.</em> (2004).\
Multiz is described in Blanchette <em>et al.</em> (2004).\
The alignment chaining methods behind the &quot;syntenic net&quot; are \
described in Kent <em>et al.</em> (2003).</P>\
\
<H2>Acknowledgments</H2>\
<P>\
Thanks to Brona Brejova of Cornell University for producing these predictions.\
</P>\
\
<H2>References</H2>\
<p>\
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM,\
Baertsch R, Rosenbloom K, Clawson H, Green ED, <em>et al.</em>\
<a href="https://genome.cshlp.org/content/14/4/708.abstract"\
target="_blank">Aligning multiple genomic sequences with the threaded blockset aligner</a>.\
<em>Genome Res</em>. 2004 Apr;14(4):708-15.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15060014" target="_blank">15060014</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC383317/" target="_blank">PMC383317</a>\
</p>\
\
<p>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<a href="https://www.pnas.org/content/100/20/11484"\
target="_blank">Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<p>\
Siepel A, Haussler D. \
<a href="http://compgen.cshl.edu/~acs/recomb2004.pdf"\
target="_blank">Computational identification of evolutionarily conserved \
exons</a>.\
<em>Proc. 8th Int'l Conf. on Research in Computational Molecular Biology</em>, \
177-186 (2004).\
</p>\
	genes	1	color 173,17,162\
group genes\
longLabel Exoniphy Mouse/Rat/Human/Dog\
shortLabel Exoniphy\
track exoniphy\
type genePred\
visibility hide\

FaceBase24SampleTypesAvg	FaceBase 24STypes	expRatio	FaceBase 24 Sample Types Averaged	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
<p>\
This dataset represents 24 independent samples of different regions of developing craniofacial\
structures obtained from embryonic day 8.5, 9.5, 10.5, and 11.5 mouse embryos. RNA was prepared separately from\
each sample and subjected to a custom mRNA microlabeling protocol so as to allow for hybridization\
to individual Affymetrix <a href="https://www.thermofisher.com/order/catalog/product/902119#/1_1"\
target="_blank">Mouse Genes 1.0 ST Arrays</a>. The various samples correspond to independent\
replicates from the following cell types:\
<ul>\
<li>e8.5 Paraxial Mesodem\
<li>e8.5 Floor Plate Neural Epithelium\
<li>e8.5 Hindbrain Neural Epithelium\
<li>e8.5 Non-floor Plate Neural Epithelium\
<li>e9.5 Olfactory Placode\
<li>e9.5 Otic Vesicle\
<li>e9.5 Facial Mesenchyme\
<li>e9.5 Mandibular Arch\
<li>e9.5 Maxillary Arch\
<li>e9.5 Neural Epithelium\
<li>e10.5 Rathke's Pouch\
<li>e10.5 Nasal Pit\
<li>e10.5 Mandibular Arch\
<li>e10.5 Maxillary Arch\
<li>e10.5 Mandibular Columnar Epithelium\
<li>e10.5 Maxillary Columnar Epithelium\
<li>e10.5 Lateral Nasal Process\
<li>e10.5 Medial Nasal Process\
<li>e10.5 Central Neural Epithelium\
<li>e10.5 Flanking Neural Epithelium\
<li>e10.5 Lateral Eminence Neural Epithelium\
<li>e10.5 Medial Eminence Neural Epithelium\
<li>e11.5 Medial Nasal Prominence\
</ul>\
</p>\
\
<h2>Display Conventions</h2>\
<p>\
In dense mode, the track color denotes the average signal over all experiments on a log base 2 scale.\
Lighter colors correspond to lower signals and darker colors correspond to higher signals. In full\
mode, the color of each item represents the log base 2 ratio of the signal of that particular\
experiment to the median signal of all experiments for that probe.\
</p>\
\
<h2>Methods</h2>\
<p>\
Microarry data was subjected to\
<a href="https://academic.oup.com/biostatistics/article/4/2/249/245074/Exploration-normalization-\
and-summaries-of-high" target="_blank">RMA normalization</a>\
and individual gene expression levels per probeset per sample\
were expressed as a ratio relative to the level of that probeset's expression using whole Postnatal\
day 1 mouse RNA as a universal reference. Colored blocks extend over the length of the corresponding\
gene and depict expression in the craniofacial sample relative to that in the reference RNA sample.\
</p>\
\
<h2>Credits</h2>\
<p>\
This track was created with the help of the following people:\
<ul>\
<li>Dissections, RNA purification, and labeling were carried out by Eric Brunskill and Steven Potter.\
<li>Hybridization and processing by Sean Smith and Hung-Chi Liang in the Cincinnati Children's Hospital\
gene expression analysis core.\
<li>Data was analyzed and transformed into UCSC genome browser array\
format by Andrew Plassard and Bruce Aronow.\
</ul>\
\
<p>\
This work was part of the <a href="https://www.facebase.org/node/154" target="_blank"\
>Global Gene Expression Atlas of Craniofacial Development</a> project being\
carried out by the <a href="https://www.facebase.org/" target="_blank">Facebase Consortium</a>.\
</p>\
\
Contact: <A HREF="mailto:&#66;&#114;&#117;&#99;e.\
&#65;&#114;&#111;n&#111;&#119;&#64;&#99;&#99;&#104;m&#99;.\
&#111;&#114;g">\
&#66;&#114;&#117;&#99;e.&#65;&#114;&#111;n&#111;&#119;&#64;&#99;&#99;&#104;m&#99;.&#111;&#114;g</A>\
<!-- above address is Bruce.Aronow at cchmc.org -->\
\
\
<h2>References</h2>\
<p>\
Brunskill EW, Potter AS, Distasio A, Dexheimer P, Plassard A, Aronow BJ, Potter SS.\
<a href="https://www.sciencedirect.com/science/article/pii/S0012160614002231" target="_blank">\
A gene expression atlas of early craniofacial development</a>.\
<em>Dev Biol</em>. 2014 Jul 15;391(2):133-46.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24780627" target="_blank">24780627</a>\
</p>\
	regulation	1	expScale 1.50\
expStep 0.1\
group regulation\
groupings facebase31_AllGroups\
longLabel FaceBase 24 Sample Types Averaged\
shortLabel FaceBase 24STypes\
track FaceBase24SampleTypesAvg\
type expRatio\
visibility hide\

wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep2	Fore Limb Bud H 2	broadPeak	Fore Limb Bud DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	100	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Fore Limb Bud DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Fore Limb Bud H 2\
subGroups view=Hotspots age=E11HALF cellType=FLBUD sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseFlbudCd1ME11halfHotspotsRep2\
type broadPeak\

wgEncodeFsuRepliChip	FSU Repli-chip	bigWig	Replication Timing by Repli-chip from ENCODE/FSU	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
\
<p>This track was produced as part of the ENCODE Project.\
This track shows genome-wide assessment of DNA replication timing in\
<A TARGET=_BLANK HREF="/cgi-bin/hgEncodeVocab?type=cellType">cell lines</A>\
using NimbleGen tiling CGH microarrays. Each experiment represents\
the relative enrichment of early vs. late S-phase nascent strands in\
a given cell line, with data represented as a loess-smoothed function\
of individual timing values at probes spaced at even intervals across \
the genome. Regions with high values indicate domains of early replication where\
initiaion occurs earlier in S-phase or early in a higher proportion of cells. \
</p>\
\
<h2>Display Conventions and Configuration</h2>\
<p>\
<DT><I>Wavelet-smoothed Signal</I></DT>\
<DD>Wavelet-smoothed of mean early/late S-phase ratios.</DD>\
</p>\
\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of\
subtracks.</p>\
\
\
<h2>Methods</h2>\
\
<p>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
Methods for replication timing profile creation and analysis are described in detail in \
Hiratani<em> et al.</em> (2008) and Ryba <em>et al.</em> (June 2011).\
Methods for individual stages are summarized below:\
</p>\
\
<h3>Extraction protocol</h3>\
\
<p>\
Replication timing data were obtained by hybridizing early and late replication intermediates to\
NimbleGen oligonucleotide arrays. Replication intermediates were prepared from cells that were first\
pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages\
of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted\
(nascent) replication intermediates that were synthesized either early or late during S-phase.\
Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification\
(WGA; Sigma, GenomePlex). \
</p>\
\
<h3>Hybridization protocol</h3>\
\
<p>\
The hydridization set used the\
<a href="https://sequencing.roche.com/en/products-solutions/by-category/target-enrichment/hybridization.html"\
target=_blank> NimbleGen standard protocol</a>. \
Cy3- and Cy5-labeled DNA samples (6 &micro;g each) were co-hybridized to Nimblegen CGH arrays \
containing evenly-spaced oligonucleotide probes across the mouse genome, with a median probe spacing\
of 1.1-5.8 kb. No differences in smoothed data have been detected with probe densities from 100 bp\
to 5.8 kb. \
</p>\
\
<h3>Scan protocol</h3>\
\
<p>\
NimbleGen MS 200 2 &micro;m resolution scanner and GenePix software were used per\
<a href="https://sequencing.roche.com/en/products-solutions/by-category/target-enrichment/hybridization.html"\
target=_blank> NimbleGen's standard protocol</a>.\
</p>\
\
<h3>Data processing</h3>\
\
<p>\
NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. \
Raw early/late data (i.e., from .pair files) from two independent biological replicates in \
which early- and late-replicating DNA were labeled reciprocally were loess-normalized to remove\
signal intensity-dependent bias, scaled to a reference data set to have the same median absolute\
deviation and then averaged (limma package, R/Bioconductor). The mean early/late ratios were used to\
generate a smoothed profile (i.e., processed data) using local polynomial smoothing (loess, 300 kb\
span) for each chromosome using basic functions in the statistical language R. \
</p>\
\
\
<h2>Verification</h2>\
\
<p>\
Technical data quality was assessed by verifying high auto-correlation between neighboring timing\
values. Biological identity was confirmed by verifying consistent early or late replication by PCR\
at individual loci, as well as uniformity in replication profiles between replicate experiments.\
</p>\
\
<h2>Credits</h2>\
\
<p>These data were generated by the FSU ENCODE group. </p>\
<p>Contact: <A HREF="mailto:&#103;&#105;&#108;b&#101;r&#116;&#64;&#98;&#105;&#111;.&#102;&#115;&#117;.&#101;du">\
David M. Gilbert</A>\
<!-- above address is gilbert at bio.fsu.edu -->\
</p>\
\
<h2>References</h2>\
\
<p>\
Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19952138"\
target="_blank">\
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis</a>.\
<em>Genome Res</em>. 2010 Feb;20(2):155-69.\
</p>\
\
<p>\
Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Sch&#252;beler D, Gilbert DM.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18842067"\
target="_blank">\
Global reorganization of replication domains during embryonic stem cell differentiation</a>.\
<em>PLoS Biol</em>. 2008 Oct 7;6(10):e245.\
</p>\
\
<p>\
Pope BD, Tsumagari K, Battaglia D, Ryba T, Hiratani I, Ehrlich M, Gilbert DM.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/22096571"\
target="_blank">\
DNA replication timing is maintained genome-wide in primary human myoblasts independent of D4Z4 contraction in FSH muscular dystrophy</a>.\
<em>PLoS One</em>. 2011;6(11):e27413.\
</p>\
\
<p>\
Ryba T, Battaglia D, Pope BD, Hiratani I, Gilbert DM.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21637205"\
target="_blank">\
Genome-scale analysis of replication timing: from bench to bioinformatics</a>.\
<em>Nat Protoc</em>. 2011 Jun;6(6):870-95.\
</p>\
\
<p>\
Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20430782"\
target="_blank">\
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types</a>.\
<em>Genome Res</em>. 2010 Jun;20(6):761-70.\
</p>\
\
<p>\
Ryba T, Hiratani I, Sasaki T, Battaglia D, Kulik M, Zhang J, Dalton S, Gilbert DM.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/22028635"\
target="_blank">\
Replication timing: a fingerprint for cell identity and pluripotency</a>.\
<em>PLoS Comput Biol</em>. 2011 Oct;7(10):e1002225.\
</p>\
\
\
<h2> Data Release Policy </h2>\
\
<p>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column, above.  The full data release policy\
for ENCODE is available\
<A TARGET=_BLANK HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</p>\
\
	regulation	0	compositeTrack on\
controlledVocabulary encode/cv.ra cellType=cell sex=sex treatment=treatment\
dimensions dimensionX=cellType dimensionY=rep dimensionZ=treatment\
dragAndDrop subTracks\
fileSortOrder cell=Cell_Line sex=Sex treatment=Treatment replicate=Rep view=View platform=Platform labExpId=Lab_ID dccAccession=UCSC_Accession geoSampleAccession=GEO_Accession fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until\
filterComposite dimZ=all\
group regulation\
longLabel Replication Timing by Repli-chip from ENCODE/FSU\
priority 0\
shortLabel FSU Repli-chip\
sortOrder cellType=+ sex=+ treatment=+ rep=+ view=+\
subGroup1 view Views WaveSignal=WaveSignal\
subGroup2 cellType Cell_Line CH12=CH12 EPISC5=EpiSC-5 EPISC7=EpiSC-7 ES46C=ES-46C ESD3=ES-D3 ESEM5S=ES-EM5Sox17huCD25 ESTT2=ES-TT2 J185A=J185a L1210=L1210 MEF=MEF MEL=MEL\
subGroup3 sex Sex M=M F=F U=U\
subGroup4 treatment Treatment NONE=None DIFFE3D=diffProtE_3_d DIFFF9D=diffProtF_9_d DIFFE6D=diffProtE_6_d DIFFE9D=diffProtE_9_d DIFFF6D=diffProtF_6_d DIFFG3D=diffProtG_3_d DIFFHSOXP=diffProtH_Sox17+ DIFFHSOXM=diffProtH_Sox17-\
subGroup5 rep Rep rep1=1 rep2=2\
track wgEncodeFsuRepliChip\
type bigWig\
viewLimits -2:2\
visibilityViewDefaults WaveSignal=hide\
windowingFunction mean+whiskers\

gap	Gap	bed 3 +	Gap Locations	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
This track depicts gaps in the assembly.  These gaps - with the\
exception of intractable centromere gaps - will be closed during the\
finishing process. \
</P><P>\
Gaps are represented as black boxes in this track.\
If the relative order and orientation of the contigs on either side\
of the gap is known, it is a <em>bridged</em> gap and a white line is drawn \
through the black box representing the gap. \
</P>\
<P>This assembly contains the following principal types of gaps:\
<UL>\
<LI><B>Fragment</B> - gaps between the contigs of a draft clone.\
(In this context, a contig is a set of overlapping sequence reads.)\
<LI><B>Contig</B> - gaps between map contigs.\
<LI><B>Centromere</B> - gaps from centromeres (3,000,000 <em>N</em>s) or \
other large blocks of heterochromatin (size varies).\
</UL></P>\
	map	1	group map\
longLabel Gap Locations\
shortLabel Gap\
track gap\
type bed 3 +\
visibility hide\

gc5Base	GC Percent	wig 0 100	GC Percent in 5-Base Windows	0	100	0	0	0	128	128	128	0	0	0			<h2>Description</h2>\
<p>\
The GC percent track shows the percentage of G (guanine) and C (cytosine) bases\
in 5-base windows.  High GC content is typically associated with\
gene-rich areas.\
</p>\
<p>\
This track may be configured in a variety of ways to highlight different\
apsects of the displayed information. Click the\
&quot;Graph configuration help&quot;\
link for an explanation of the configuration options.\
\
<h2>Credits</h2>\
<p> The data and presentation of this graph were prepared by\
<a href="mailto:&#104;&#105;&#114;a&#109;&#64;&#115;&#111;&#101;\
.&#117;&#99;&#115;&#99;.&#101;&#100;u">Hiram Clawson</a>.\
</p>\
\
	map	0	altColor 128,128,128\
autoScale Off\
color 0,0,0\
graphTypeDefault Bar\
gridDefault OFF\
group map\
longLabel GC Percent in 5-Base Windows\
maxHeightPixels 128:36:16\
shortLabel GC Percent\
spanList 5\
track gc5Base\
type wig 0 100\
viewLimits 30:70\
visibility hide\
windowingFunction Mean\

igtc	Gene Trap	psl .	International Gene Trap Consortium Sequence Tag Alignments	0	100	0	0	0	127	127	127	0	0	0		http://www.genetrap.org/cgi-bin/annotation.py?cellline=$$	<H2>Description</H2>\
<P>\
This track shows alignments of \
<A HREF="https://igtc.org/" TARGET=_BLANK>International Gene Trap \
Consortium</A> sequence tags to the mouse genome.  \
Items are labeled by cell line and colored by source:\
<TABLE BORDERWIDTH=0>\
<TR><TD><B><FONT COLOR="#9900CC">BG</FONT></B>:</TD>\
    <TD><A HREF="https://igtc.org/" TARGET=_BLANK>BayGenomics</A>\
        (USA)</TD></TR>\
<TR><TD><B><FONT COLOR="#0000CC">CMHD</FONT></B>:</TD>\
    <TD><A HREF="http://www.cmhd.ca/genetrap/index.html" TARGET=_BLANK>Centre \
        for Modeling Human Disease</A> (Toronto, Canada)</TD></TR>\
<TR><TD><B><FONT COLOR="#6699FF">EGTC</FONT></B>:</TD>\
    <TD><A HREF="http://egtc.jp/action/main/index" TARGET=_BLANK>Exchangeable Gene\
        Trap Clones</A> (Kumamoto University, Japan)</TD></TR>\
<TR><TD><B><FONT COLOR="#00CC00">ESDB</FONT></B>:</TD>\
    <TD>Embryonic Stem Cell Database (University of Manitoba, Canada)</TD></TR>\
<TR><TD><B><FONT COLOR="#CC9900">FHCRC</FONT></B>:</TD>\
    <TD><A HREF="https://labs.icahn.mssm.edu/sorianolab/gene-trap/gene-trap-mutagenesis/"\
        TARGET=_BLANK>Soriano Lab Gene Trap Database</A>\
        (originally at Fred Hutchinson Cancer Research Center, Seattle, USA;\
        now at Mount Sinai School of Medicine, Manhattan, NY)</TD></TR>\
<TR><TD><B><FONT COLOR="#FF9900">GGTC</FONT></B>:</TD>\
    <TD><A HREF="http://www.genetrap.de" TARGET=_BLANK>German Gene Trap \
        Consortium</A> (Germany)</TD></TR>\
<TR><TD><B><FONT COLOR="#996600">SIGTR</FONT></B>:</TD>\
    <TD><A HREF="https://www.sanger.ac.uk/science/collaboration/sanger-institute-gene-trap-resource"\
        TARGET=_BLANK>Sanger Institute Gene Trap Resource</A> \
        (Cambridge, UK)</TD></TR>\
<TR><TD><B><FONT COLOR="#CC0000">TIGEM</FONT></B>:</TD>\
    <TD><A HREF="https://www.tigem.it/"\
        TARGET=_BLANK>TIGEM-IRBM Gene Trap</A> (Naples, Italy)</TD></TR>\
<TR><TD><B><FONT COLOR="#AA0066">TIGM</FONT></B>:</TD>\
    <TD><A HREF="https://www.tigm.org/" \
        TARGET=_BLANK>Texas Institute for Genomic Medicine</A> (Houston, Texas)</TD></TR>\
</TABLE>\
</P>\
\
<H2>Methods</H2>\
<P>\
The \
<A HREF="https://igtc.org/info/pipeline.html" TARGET=_BLANK>IGTC \
pipeline</A>\
uses BLAT to align sequence tags from dbGSS to the mouse genome and \
BLAST to match sequence tags to genes.  The pipeline filters and reconciles \
the two sets of alignments to associate cell lines with trapped genes.  \
</P>\
\
<H2>Credits</H2>\
<P>\
Thanks to the \
<A HREF="https://igtc.org/" TARGET=_BLANK>International Gene Trap \
Consortium</A> for providing this track.\
</P>\
	genes	1	group genes\
longLabel International Gene Trap Consortium Sequence Tag Alignments\
shortLabel Gene Trap\
track igtc\
type psl .\
url http://www.genetrap.org/cgi-bin/annotation.py?cellline=$$\
urlLabel IGTC Cell Line Annotation:\
visibility hide\

geneid	Geneid Genes	genePred geneidPep	Geneid Gene Predictions	0	100	0	90	100	127	172	177	0	0	0			<h2>Description</h2>\
\
<p>\
This track shows gene predictions from the\
<a href="https://genome.crg.cat/software/geneid/index.html"\
target="_blank">geneid</a> program developed by\
<a href="https://www.crg.eu/roderic_guigo"\
target="_blank">Roderic Guig&oacute;'s Computational Biology of RNA Processing</a>\
group which is part of the\
<a href="https://www.crg.eu/" target="_blank">Centre de Regulaci&oacute; Gen&ograve;mica</a>\
(CRG) in Barcelona, Catalunya, Spain.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
Geneid is a program to predict genes in anonymous genomic sequences designed\
with a hierarchical structure. In the first step, splice sites, start and stop\
codons are predicted and scored along the sequence using Position Weight Arrays\
(PWAs). Next, exons are built from the sites. Exons are scored as the sum of the\
scores of the defining sites, plus the the log-likelihood ratio of a\
Markov Model for coding DNA. Finally, from the set of predicted exons, the gene\
structure is assembled, maximizing the sum of the scores of the assembled exons.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
Thanks to <a href="https://www.crg.eu/roderic_guigo"\
target="blank">Computational Biology of RNA Processing</a>\
for providing these data.\
\
</p>\
\
<h2>References</h2>\
<p>\
Blanco E, Parra G, Guig&#243; R.\
<a href="https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471250953.bi0403s18"\
target="_blank">Using geneid to identify genes</a>.\
<em>Curr Protoc Bioinformatics</em>. 2007 Jun;Chapter 4:Unit 4.3.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18428791" target="_blank">18428791</a>\
</p>\
\
\
<p>\
Parra G, Blanco E, Guig&#243; R.\
<a href="https://genome.cshlp.org/content/10/4/511.long" target="_blank">\
GeneID in Drosophila</a>.\
<em>Genome Res</em>. 2000 Apr;10(4):511-5.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/10779490" target="_blank">10779490</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310871/" target="_blank">PMC310871</a>\
</p>\
	genes	1	color 0,90,100\
group genes\
longLabel Geneid Gene Predictions\
shortLabel Geneid Genes\
track geneid\
type genePred geneidPep\
visibility hide\

genscan	Genscan Genes	genePred genscanPep	Genscan Gene Predictions	0	100	170	100	0	212	177	127	0	0	0			<h2>Description</h2>\
\
<p>\
This track shows predictions from the\
<a href="http://hollywood.mit.edu/GENSCAN.html" target="_blank">Genscan</a> program\
written by <a href="https://www.genes.mit.edu/chris" target="_blank">Chris Burge</a>.\
The predictions are based on transcriptional, translational and donor/acceptor\
splicing signals as well as the length and compositional distributions of exons,\
introns and intergenic regions.\
</p>\
\
<p>\
For more information on the different gene tracks, see our <a target=_blank \
href="/FAQ/FAQgenes.html">Genes FAQ</a>.</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track follows the display conventions for\
<a href="/goldenPath/help/hgTracksHelp.html#GeneDisplay" target="_blank">gene prediction\
tracks</a>.\
</p>\
\
<p>\
The track description page offers the following filter and configuration\
options:\
<ul>\
<li><b>Color track by codons:</b> Select the <em>genomic codons</em> option\
to color and label each codon in a zoomed-in display to facilitate validation\
and comparison of gene predictions. Go to the\
<a HREF="/goldenPath/help/hgCodonColoring.html" target="_blank">\
Coloring Gene Predictions and Annotations by Codon</a> page for more\
information about this feature.</li>\
</ul>\
</p>\
\
<h2>Methods</h2>\
\
<p>\
For a description of the Genscan program and the model that underlies it,\
refer to Burge and Karlin (1997) in the References section below.\
The splice site models used are described in more detail in Burge (1998)\
below.\
</p>\
\
<h2>Credits</h2>\
\
Thanks to Chris Burge for providing the Genscan program.\
\
<h2>References</h2>\
\
<p>\
Burge C.\
Modeling Dependencies in Pre-mRNA Splicing Signals.\
In: Salzberg S, Searls D, Kasif S, editors.\
<a href="https://www.elsevier.com/books/computational-methods-in-molecular-biology/salzberg/978-0-444-82875-0"\
target="_blank">Computational Methods in Molecular Biology</a>.\
Amsterdam: Elsevier Science; 1998. p. 127-163.\
</p>\
\
<p>\
Burge C, Karlin S.\
<a href="https://www.sciencedirect.com/science/article/pii/S0022283697909517" target="_blank">\
Prediction of complete gene structures in human genomic DNA</a>.\
<em>J. Mol. Biol.</em> 1997 Apr 25;268(1):78-94.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/9149143" target="_blank">9149143</a>\
</p>\
	genes	1	color 170,100,0\
group genes\
longLabel Genscan Gene Predictions\
shortLabel Genscan Genes\
track genscan\
type genePred genscanPep\
visibility hide\

gnfAtlas2	GNF Atlas 2	expRatio	GNF Expression Atlas 2	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>This track shows expression data from the GNF Gene Expression\
Atlas 2. This contains two replicates each of 61 mouse \
tissues run over Affymetrix microarrays.\
By default, averages of related tissues are shown.  Display all tissues\
by selecting &quot;All Arrays&quot; from the &quot;Combine arrays&quot; menu\
on the track settings page.\
As is standard with microarray data red indicates overexpression in the \
tissue, and green indicates underexpression.   You may want to view gene\
expression with the Gene Sorter as well as the Genome Browser.</P>\
\
<H2>Credits</H2>\
Thanks to the \
<A HREF="https://www.gnf.nibr.com//" TARGET=_blank>Genomics Institute of the Novartis \
Research Foundation</A> (GNF) for the data underlying this track.  \
\
<H2>References</H2>\
<p>\
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G\
<em>et al</em>.\
<A HREF="https://www.pnas.org/content/101/16/6062" TARGET=_blank>\
A gene atlas of the mouse and human protein-encoding transcriptomes</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2004 Apr 20;101(16):6062-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15075390" target="_blank">15075390</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC395923/" target="_blank">PMC395923</a>\
</p>\
	regulation	1	expScale 4.0\
expStep 0.5\
expTable gnfMouseAtlas2MedianExps\
group regulation\
groupings gnfMouseAtlas2Groups\
longLabel GNF Expression Atlas 2\
shortLabel GNF Atlas 2\
track gnfAtlas2\
type expRatio\
visibility hide\

affyGnfU74A	GNF U74A	expRatio	GNF Expression Atlas on Mouse Affymetrix U74A Chip	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track shows expression data from <a href="https://www.gnf.nibr.com/"\
TARGET=_blank">GNF</A> (The Genomics Institute of the Novartis Research \
Foundation) using the <A HREF="https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html"\
TARGET=_blank>Affymetrix</A> U74A chip. </P>\
\
<H2>Methods</H2>\
<P>\
For detailed information about the experiments, see Su <em>et al.</em> (2002)\
in the References section below. Alignments displayed on the track correspond \
to the consensus sequences used by Affymetrix to choose probes.</P> \
<P>\
In dense mode, the track color denotes the average signal over all\
experiments on a log base 2 scale. Lighter colors correspond to lower signals;\
darker colors correspond to higher signals. In full\
mode, the color of each item represents the log base 2 ratio of the signal of\
that particular experiment to the median signal of all experiments for that \
probe.</P>\
<P>\
More information about individual probes and probe sets is available at\
Affymetrix's <A HREF="http://www.affymetrix.com/analysis/index.affx"\
TARGET=_blank>NetAffx</A> website. </P>\
\
<H2>Credits</H2>\
<P>\
Thanks to GNF for providing these data. </P>\
\
<H2>References</H2>\
<p>\
Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A\
<em>et al</em>.\
<a href="https://www.pnas.org/content/99/7/4465" target="_blank">\
Large-scale analysis of the human and mouse transcriptomes</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2002 Apr 2;99(7):4465-70.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11904358" target="_blank">11904358</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC123671/" target="_blank">PMC123671</a>\
</p>\
	regulation	1	expScale 4.0\
expStep 0.5\
expTable gnfMouseU74aAllExps\
group regulation\
groupings gnfMouseU74aGroups\
longLabel GNF Expression Atlas on Mouse Affymetrix U74A Chip\
shortLabel GNF U74A\
track affyGnfU74A\
type expRatio\
visibility hide\

affyGnfU74B	GNF U74B	expRatio	GNF Expression Atlas on Mouse Affymetrix U74B Chip	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track shows expression data from <a href="https://www.gnf.nibr.com/"\
TARGET=_blank">GNF</A> (The Genomics Institute of the Novartis Research \
Foundation) using the <A HREF="https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html"\
TARGET=_blank>Affymetrix</A> U74B chip. </P>\
\
<H2>Methods</H2>\
<P>\
For detailed information about the experiments, see Su <em>et al.</em> (2002)\
in the References section below. Alignments displayed on the track\
correspond to the consensus sequences used by Affymetrix to choose probes.</P>\
\
<P>\
In dense mode, the track color denotes the average signal over all\
experiments on a log base 2 scale. Lighter colors correspond to lower signals;\
darker colors correspond to higher signals. In full\
mode, the color of each item represents the log base 2 ratio of the signal of\
that particular experiment to the median signal of all experiments for that \
probe.</P>\
<P>\
More information about individual probes and probe sets is available at\
Affymetrix's <A HREF="http://www.affymetrix.com/analysis/index.affx"\
TARGET=_blank>NetAffx</A> website. </P>\
\
<H2>Credits</H2>\
<P>\
Thanks to GNF for providing these data. </P>\
\
<H2>References</H2>\
<p>\
Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A\
<em>et al</em>.\
<a href="https://www.pnas.org/content/99/7/4465" target="_blank">\
Large-scale analysis of the human and mouse transcriptomes</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2002 Apr 2;99(7):4465-70.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11904358" target="_blank">11904358</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC123671/" target="_blank">PMC123671</a>\
</p>\
	regulation	1	expScale 4.0\
expStep 0.5\
expTable gnfMouseU74bAllExps\
group regulation\
groupings gnfMouseU74bGroups\
longLabel GNF Expression Atlas on Mouse Affymetrix U74B Chip\
shortLabel GNF U74B\
track affyGnfU74B\
type expRatio\
visibility hide\

affyGnfU74C	GNF U74C	expRatio	GNF Expression Atlas on Mouse Affymetrix U74C Chip	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track shows expression data from <a href="https://www.gnf.nibr.com/"\
TARGET=_blank">GNF</A> (The Genomics Institute of the Novartis Research \
Foundation) using the <A HREF="https://www.thermofisher.com/us/en/home/life-science/microarray-analysis.html"\
TARGET=_blank>Affymetrix</A> U74C chip. </P>\
\
<H2>Methods</H2>\
<P>\
For detailed information about the experiments, see Su <em>et al.</em> (2002)\
in the References section below. Alignments displayed on the track correspond \
to the consensus sequences used by Affymetrix to choose probes.</P> \
<P>\
In dense mode, the track color denotes the average signal over all\
experiments on a log base 2 scale. Lighter colors correspond to lower signals \
and darker colors correspond to higher signals. In full\
mode, the color of each item represents the log base 2 ratio of the signal of\
that particular experiment to the median signal of all experiments for that \
probe.</P>\
<P>\
More information about individual probes and probe sets is available at\
Affymetrix's <A HREF="http://www.affymetrix.com/analysis/index.affx"\
TARGET=_blank>NetAffx</A> website. </P>\
\
<H2>Credits</H2>\
<P>\
Thanks to GNF for providing these data. </P>\
\
<H2>References</H2>\
<p>\
Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A\
<em>et al</em>.\
<a href="https://www.pnas.org/content/99/7/4465" target="_blank">\
Large-scale analysis of the human and mouse transcriptomes</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2002 Apr 2;99(7):4465-70.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11904358" target="_blank">11904358</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC123671/" target="_blank">PMC123671</a>\
</p>\
	regulation	1	expScale 4.0\
expStep 0.5\
expTable gnfMouseU74cAllExps\
group regulation\
groupings gnfMouseU74cGroups\
longLabel GNF Expression Atlas on Mouse Affymetrix U74C Chip\
shortLabel GNF U74C\
track affyGnfU74C\
type expRatio\
visibility hide\

grcIncidentDb	GRC Incident	bigBed 4 +	GRC Incident Database	0	100	0	0	0	127	127	127	0	0	0		https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=$$	<H2>Description</H2>\
<P>\
This track shows locations in the mouse assembly where assembly\
problems have been noted or resolved, as reported by the\
<A HREF="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/index.shtml"\
TARGET="_blank">Genome Reference Consortium</A> (GRC). \
</P>\
<P>\
If you would like to report an assembly problem, please use the GRC\
<A HREF="https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/ReportAnIssue.shtml"\
TARGET="_blank">issue reporting system</A>.\
</P>\
\
<H2>Methods</H2>\
<P>\
Data for this track are extracted from the GRC\
<A HREF="ftp://ftp.ncbi.nlm.nih.gov/pub/grc/" TARGET="_blank">incident database</A> from the specific species *_issues.gff3 file.\
The track is synchronized once daily to incorporate new updates. \
</P>\
\
<H2>Credits</H2>\
<P> The data and presentation of this track were prepared by\
<A HREF="mailto:&#104;&#105;&#114;a&#109;&#64;&#115;&#111;&#101;\
.&#117;&#99;&#115;&#99;.&#101;&#100;u">Hiram Clawson</A>.\
</P>\
	map	1	group map\
longLabel GRC Incident Database\
shortLabel GRC Incident\
track grcIncidentDb\
type bigBed 4 +\
url https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/issue_detail.cgi?id=$$\
urlLabel GRC Incident:\
visibility hide\

wgEncodeLicrHistoneHeartH3k36me3MAdult8wksC57bl6StdSig	Heart 8w H3K36m3	bigWig 0.110000 18.590000	Heart 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	100	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 8w H3K36m3\
subGroups view=Signal age=A1DLT8W factor=H3K36ME3 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k36me3MAdult8wksC57bl6StdSig\
type bigWig 0.110000 18.590000\
viewLimits 0.2:2\

wgEncodeUwDnaseViewHotspots	Hot Spots	bed 3	DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington\
pValueFilter 0.0\
pValueFilterLimits 1:324\
parent wgEncodeUwDnase\
scoreFilter 100\
scoreFilterLimits 100:1000\
scoreMin 0\
shortLabel Hot Spots\
track wgEncodeUwDnaseViewHotspots\
view Hotspots\
visibility pack\

wgEncodeUwDgfViewHotspots	Hotspots	bed 3	DNaseI Digital Genomic Footprinting from ENCODE/University of Washington	0	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel DNaseI Digital Genomic Footprinting from ENCODE/University of Washington\
minGrayLevel 2\
pValueFilter 0.0\
pValueFilterLimits 1:324\
parent wgEncodeUwDgf\
scoreFilter 100\
scoreFilterLimits 100:1000\
shortLabel Hotspots\
track wgEncodeUwDgfViewHotspots\
view Hotspots\
visibility hide\

ikmc	IKMC Genes	bed 12	International Knockout Mouse Consortium Genes	0	100	0	0	0	127	127	127	0	0	0		http://www.mousephenotype.org/data/genes/$$	<H3>Description</H3>\
<P>\
This track shows genes targeted by \
<A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/about"\
TARGET=_BLANK>International Knockout Mouse Consortium (IKMC)</A>, a \
collaboration to generate a public resource of mouse embryonic stem (ES)\
cells containing a null mutation in every gene in the mouse genome.\
Gene targets are color-coded by status:\
<UL>\
<LI><span style="color: #00F000; font-weight: bold;">Green</span>: Reagent(s) Available</LI>\
<LI><span style="color: #FFD000; font-weight: bold;">Yellow</span>: In Progress</LI>\
<LI><span style="color: #0000C8; font-weight: bold;">Blue</span>: Not Started/On Hold</LI>\
<LI><span style="color: #000; font-weight: bold;">Black</span>: Withdrawn/Problematic</LI>\
</UL>\
</P>\
<P>\
The <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/aboutkompdcc" TARGET=_BLANK>KnockOut Mouse Project Data\
Coordination Center (KOMP DCC)</A> is the central database resource\
for coordinating mouse gene targeting within IKMC and provides\
web-based query and display tools for IKMC data.  In addition, the\
KOMP DCC website provides a tool for the scientific community to\
nominate genes of interest to be knocked out by the KOMP initiative.</P>\
\
<P>\
IKMC members include\
<UL>\
<LI><a href="https://www.mousephenotype.org/martsearch_ikmc_project/aboutkomp" TARGET=_BLANK>KnockOut\
    Mouse Project (KOMP)</a>, a trans-NIH initiative (USA)</LI>\
<LI><a href="https://www.mousephenotype.org/about-impc/about-ikmc/eucomm/" TARGET=_BLANK>European\
    Conditional Mouse Mutagenesis Program (EUCOMM)</a>, funded by the\
    European Union Framework 6 programme (EU)</LI>\
<LI><a href="http://norcomm.org/index.htm"\
    TARGET=_BLANK>North American Conditional Mouse Mutagenesis Project\
    (NorCOMM)</a>, a Genome Prairie Project (Canada)</LI>\
<LI><a href="https://www.tigm.org/" TARGET=_BLANK>Texas A&amp;M\
    Institute for Genomic Medicine (TIGM)</a> (USA)</LI>\
</UL>\
\
KOMP includes two production centers: \
CSD, a collaborative team at the <A HREF="http://www.chori.org/drupal1/"\
TARGET=_BLANK>Children's Hospital Oakland Research Institute\
(CHORI)</A>, the <A HREF="https://www.sanger.ac.uk/research/projects/genetrap/"\
TARGET=_BLANK>Wellcome Trust Sanger Institute</A> and the University\
of California at Davis <A HREF="https://www.vetmed.ucdavis.edu/"\
TARGET=_BLANK>School of Veterinary Medicine</A>, and \
a team at the <A HREF="https://www.regeneron.com/technology"\
TARGET=_BLANK>VelociGene</A> division of Regeneron Pharmaceuticals, Inc.\
EUCOMM includes <A HREF="https://www.mousephenotype.org/about-impc/about-ikmc/eucomm/"\
TARGET=_BLANK>9 participating institutions</A>.  \
NorCOMM includes several <A HREF="http://norcomm.org/research_partners.htm" \
TARGET=_BLANK>participating institutions</A>.\
</P>\
<P>\
Items displayed as a solid box represent the gene regions targeted by\
the Regeneron gene knockout strategy.  In most cases Regeneron alleles\
will be complete null alleles that delete the entire protein coding\
sequence of the target gene.</P>\
<P>\
Items displayed as lines connecting short boxes represent the\
targeting vector construct strategy used by EuCOMM, NorCOMM, and\
CSD. This strategy relies on the identification of a\
&quot;critical&quot; exon common to all transcript variants that, when\
deleted, creates a frame-shift mutation.  The short boxes in the middle \
of an item show the vector features that surround the critical exon.\
</P>\
\
<H3>Methods</H3>\
<P>\
Using <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/aboutkompstrategies"\
TARGET=_BLANK>complementary targeting strategies</A>, the IKMC centers \
design and create targeting vectors, mutant ES cell lines and, to some\
extent, mutant mice, embryos or sperm. Materials are distributed to\
the research community.</P>\
<P>\
The <A HREF="https://www.komp.org/index.php?link=5" TARGET=_BLANK>KOMP Repository</A> \
archives, maintains, and distributes IKMC products. Researchers can\
order products and get product information from the\
Repository. Researchers can also express interest in products that are\
still in the pipeline. They will then receive email notification as\
soon as KOMP generated products are available for distribution.</P>\
<P>\
The process for ordering EUCOMM materials can be found \
<A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/about/eucomm" TARGET=_BLANK>here</A>.</P>\
<P>\
The process for ordering TIGM materials can be found \
<A HREF="https://www.tigm.org/repository/" TARGET=_BLANK>here</A>.</P>\
<P>\
Information on NorCOMM products and services can be found \
<A HREF="http://norcomm.org/accessing_services.htm"\
TARGET=_BLANK>here</A>.</P>\
\
<H3>Credits</H3>\
<P>\
Thanks to the <A HREF="https://www.mousephenotype.org/martsearch_ikmc_project/about"\
TARGET=_BLANK>International Knockout Mouse Consortium</A>, and Carol Bult in \
particular, for providing these data.</P>\
\
<H3>References</H3>\
<p>\
Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig\
JT <em>et al</em>.\
<a href="https://www.nature.com/articles/ng0904-921" target="_blank">\
The knockout mouse project</a>.\
<em>Nat Genet</em>. 2004 Sep;36(9):921-4.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15340423" target="_blank">15340423</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716027/" target="_blank">PMC2716027</a>\
</p>\
\
<p>\
Collins FS, Finnell RH, Rossant J, Wurst W.\
<a href="https://www.sciencedirect.com/science/article/pii/S0092867407004643" target="_blank">\
A new partner for the international knockout mouse consortium</a>.\
<em>Cell</em>. 2007 Apr 20;129(2):235.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17448981" target="_blank">17448981</a>\
</p>\
\
<p>\
International Mouse Knockout Consortium, Collins FS, Rossant J, Wurst W.\
<a href="https://www.sciencedirect.com/science/article/pii/S0092867406016126" target="_blank">\
A mouse for all reasons</a>.\
<em>Cell</em>. 2007 Jan 12;128(1):9-13.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17218247" target="_blank">17218247</a>\
</p>\
	genes	1	group genes\
itemRgb on\
longLabel International Knockout Mouse Consortium Genes\
mgiUrl http://www.informatics.jax.org/marker/$$\
mgiUrlLabel MGI Report:\
noScoreFilter .\
shortLabel IKMC Genes\
track ikmc\
type bed 12\
url http://www.mousephenotype.org/data/genes/$$\
urlLabel KOMP Data Coordination Center:\
visibility hide\

wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep2V2	Kidney Aln 2	bam	Kidney A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	100	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Kidney Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=KIDNEY rep=rep2\
track wgEncodeCshlLongRnaSeqKidneyAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistone	LICR Histone	bed 3	Histone Mods by ChIP-seq from ENCODE/LICR	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<P>\
This track shows a comprehensive survey of <i>cis</i>-regulatory elements\
in the mouse genome by using ChIP-seq &#40;Robertson <EM> et al.</EM>, 2007&#41; to identify\
transcription factor binding sites and chromatin modification\
profiles in various mouse &#40;C57BL/6, 129/Ola&#41; tissues, primary cells, and cell lines. \
</P> \
<P>\
The Ren lab examined RNA polymerase II &#40;PolII&#41;, \
co-activator protein p300, the insulator protein CTCF, and \
the following chromatin modification marks: H3K4me3 and H3K4me1, \
H3K27ac, H3K36me3, H3K9me3, and H3K27me3 due to their \
demonstrated utilities in identifying promoters, enhancers, \
insulator elements, actively transcribed gene bodies, and \
silent chromatin regions &#40;Barski <EM>et al.</EM>, 2007; Bernstein \
<EM>et al.</EM>, 2006; Blow <EM>et al.</EM>, 2010; \
Creyghton <EM>et al.</EM>, 2010; Francis <EM>et al.</EM>, 2004; Hawkins \
<EM>et al.</EM>, 2011; Heintzman <EM>et al.</EM>, 2009; Kim <EM>et al.\
</EM>, 2007; Kim <EM> et al.</EM>, 2005; Krogan <EM>et al.</EM>, 2003; Li \
<EM>et al.</EM>, 2002; Peters <EM> et al.</EM>, 2001; Rada-Iglesias <EM>et al.\
</EM>, 2011; Schotta <EM>et al.</EM>, 2002; Visel <EM>et al.</EM>, 2009&#41;.\
Enrichment of PolII signals is a strong indicator of \
an active promoter and the presence of p300 outside of\
promoter regions has been used as a mark for enhancers.  \
CTCF binding sites are considered as a mark for \
potential insulator elements.  H3K4me3 is an active mark \
for promoters and H3K27ac is an active mark for both promoters \
and enhancers.  In the absence of H3K4me3, H3K4me1 serves as an\
active mark for enhancers.  H3K36me3 is normally found in actively \
transcribed gene bodies whereas both H3K9me3 and H3K27me3 are common\
repressive marks for transcriptionally silent chromatin regions.\
For each transcription factor or chromatin mark in each tissue, \
ChIP-seq was carried out with at least two biological \
replicates. Each experiment produced 20-30 million uniquely-mapped monoclonal tags.\
</P>\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
<DL>\
<DT><I>Peaks</I></DT><DD> Regions of signal enrichment based on processed data\
(normalized data from pooled replicates). Intensity is represented in\
grayscale; darker shading shows higher intensity (a solid vertical line\
\	in the peak region represents the point with the highest signal).\
</DD>\
<DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based on\
processed data.</DD>\
</DL>\
</P>\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
<P>\
<!--echo var="BROWSER_HOST" -->\
Additional views are available on the Downloads page. \
</P>\
\
<H2>Methods</H2>\
\
<P>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
</P>\
\
<P><DT><B><I>Enrichment and Library Preparation</I></B></DT>\
\
Chromatin immunoprecipitation was performed according to the <A HREF="http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" \
TARGET=_BLANK>Ren Lab ChIP Protocol</A>.\
</P>\
<P>\
Library construction was performed according to the <A HREF="http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf"\
TARGET=_BLANK>Ren Lab Library Protocol</A>.\
</P>\
\
<P><DT><B><I>Sequencing and Analysis</I></B></DT>\
Samples were sequenced on Illumina Genome Analyzer II,\
Genome Analyzer IIx and HiSeq 2000 platforms\
for 36 cycles.  Image analysis, base calling and \
alignment to the mouse genome version NCBI37/mm9 were performed \
using Illumina&#39;s RTA and Genome Analyzer Pipeline software. \
Alignment to the mouse genome was performed using ELAND\
or <a href="http://bowtie-bio.sourceforge.net/index.shtml" target="_blank">\
Bowtie</a> (Langmead <EM>et al.</EM>, 2009) with \
a seed length of 25 and allowing up to two mismatches. \
Only the sequences that mapped to one location were used \
for further analysis.  Of those sequences, clonal reads,\
defined as having the same start position on the same \
strand, were discarded.  BED and wig files were\
created using custom perl scripts.\
</P>\
\
<h2>Release Notes</h2>\
\
<p>\
This is Release 3 (Aug 2012). It contains a total of 130 Chip-seq experiments on histone modifications with the addition of 31 new experiments.\
</p>\
\
<H2>Credits</H2>\
\
<P>\
These data were generated and analyzed in\
<A HREF="http://bioinformatics-renlab.ucsd.edu/rentrac/" TARGET=_BLANK>Bing Ren&#39;s laboratory</A>\
at the Ludwig Institute for Cancer Research (LICR).\
</P>\
<P>\
Contact: <A HREF="mailto:&#121;&#55;&#115;h&#101;n&#64;&#117;&#99;&#115;&#100;.\
&#101;&#100;u">Yin Shen</A>\
<!-- above address is y7shen at ucsd.edu -->\
</P>\
\
\
<H2>References</H2>\
\
<p>\
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17512414" target="_blank">\
High-resolution profiling of histone methylations in the human genome</a>.\
<em>Cell</em>. 2007 May 18;129(4):823-37.\
</p>\
\
<p>\
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/16630819" target="_blank">\
A bivalent chromatin structure marks key developmental genes in embryonic stem cells</a>.\
<em>Cell</em>. 2006 Apr 21;125(2):315-26.\
</p>\
\
<p>\
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20729851" target="_blank">\
ChIP-Seq identification of weakly conserved heart enhancers</a>.\
<em>Nat Genet</em>. 2010 Sep;42(9):806-10.\
</p>\
\
<p>\
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21106759" target="_blank">\
Histone H3K27ac separates active from poised enhancers and predicts developmental state</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2010 Dec 14;107(50):21931-6.\
</p>\
\
<p>\
Francis NJ, Kingston RE, Woodcock CL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/15567868" target="_blank">\
Chromatin compaction by a polycomb group protein complex</a>.\
<em>Science</em>. 2004 Nov 26;306(5701):1574-7.\
</p>\
\
<p>\
Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21876557" target="_blank">\
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency</a>.\
<em>Cell Res</em>. 2011 Oct;21(10):1393-409.\
</p>\
\
<p>\
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19295514" target="_blank">\
Histone modifications at human enhancers reflect global cell-type-specific gene expression</a>.\
<em>Nature</em>. 2009 May 7;459(7243):108-12.\
</p>\
\
<p>\
Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17382889" target="_blank">\
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome</a>.\
<em>Cell</em>. 2007 Mar 23;128(6):1231-45.\
</p>\
\
<p>\
Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/15899964" target="_blank">\
Direct isolation and identification of promoters in the human genome</a>.\
<em>Genome Res</em>. 2005 Jun;15(6):830-9.\
</p>\
\
<p>\
Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/12773564" target="_blank">\
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II</a>.\
<em>Mol Cell Biol</em>. 2003 Jun;23(12):4207-18.\
</p>\
\
<p>\
Langmead B, Trapnell C, Pop M, Salzberg SL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174" target="_blank">\
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>.\
<em>Genome Biol</em>. 2009;10(3):R25.\
</p>\
\
<p>\
Li J, Moazed D, Gygi SP.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/12381723" target="_blank">\
Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation</a>.\
<em>J Biol Chem</em>. 2002 Dec 20;277(51):49383-8.\
</p>\
\
<p>\
Peters AH, O'Carroll D, Scherthan H, Mechtler K, Sauer S, Sch&#246;fer C, Weipoltshammer K, Pagani M, Lachner M, Kohlmaier A <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/11701123" target="_blank">\
Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability</a>.\
<em>Cell</em>. 2001 Nov 2;107(3):323-37.\
</p>\
\
<p>\
Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21160473" target="_blank">\
A unique chromatin signature uncovers early developmental enhancers in humans</a>.\
<em>Nature</em>. 2011 Feb 10;470(7333):279-83.\
</p>\
\
<p>\
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17558387" target="_blank">\
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing</a>.\
<em>Nat Methods</em>. 2007 Aug;4(8):651-7.\
</p>\
\
<p>\
Schotta G, Ebert A, Krauss V, Fischer A, Hoffmann J, Rea S, Jenuwein T, Dorn R, Reuter G.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/11867540" target="_blank">\
Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing</a>.\
<em>EMBO J</em>. 2002 Mar 1;21(5):1121-31.\
</p>\
\
<p>\
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19212405" target="_blank">\
ChIP-seq accurately predicts tissue-specific activity of enhancers</a>.\
<em>Nature</em>. 2009 Feb 12;457(7231):854-8.\
</p>\
\
<H2>Data Release Policy</H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column, above.  The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
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wgEncodeLicrRnaSeq	LICR RNA-seq	bed 3	RNA-seq from ENCODE/LICR	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<P>\
Using RNA-seq (Mortazavi <EM>et al.</EM>, 2008), high-resolution\
genome-wide maps of the mouse transcriptome in various mouse (C57BL/6) \
tissues, primary cells, cell lines of different developmental stage and age groups were generated. \
</P>\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>\
This is a composite track that contains multiple data types\
(<EM>views</EM>). For each view, there are multiple subtracks that\
display individually on the browser. Instructions for configuring composite\
tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
<DL>\
<DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based\
on processed data.</DD>\
<DT><I>Alignments</I></DT><DD>Mappings of short reads to the genome. See the <A HREF="https://samtools.github.io/hts-specs/SAMv1.pdf" TARGET="_BLANK">SAM Format Specification</A> for more information on the SAM/BAM file format.</DD>\
</DL>\
</P>\
\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
\
<P>\
<!--echo var="BROWSER_HOST" -->\
Additional views are available on the Downloads page. \
</P>\
\
<H2>Methods</H2>\
\
<P>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
</P>\
\
<P><DT><B><I>RNA-seq</I></B></DT>\
RNA samples from tissues and primary cells were extracted\
from Trizol&#174; according to protocol (Invitrogen). Long PolyA+ RNA\
was purified with the Dynabeads mRNA purification kit (Invitrogen).\
The mRNA libraries were prepared for strand-specific sequencing as\
described previously (Parkhomchuk <EM>et al.</EM>, 2009).\
</P>\
\
\
<P><DT><B><I>Sequencing and Analysis</I></B></DT>\
Samples were sequenced on Illumina Genome Analyzer II,\
Genome Analyzer IIx and HiSeq 2000 platforms\
for 36 cycles.  Image analysis, base calling and \
alignment to the mouse genome version NCBI37/mm9 were performed \
using Illumina&#39;s RTA.\
Alignment to the mouse genome was performed using\
TopHat (Trapnell <EM>et al</EM>., 2009).  Wig files were \
generated by TopHat and expression levels were \
calculated with Cufflinks (Trapnell <EM>et al.</EM>, 2010).\
</P>\
\
<h2>Release Notes</h2>\
\
<p>\
This is Release 2 (Mar 2012). It contains a total of 22 RNA-seq experiments with the addition of 12 new experiments.\
</p>\
\
<H2>Credits</H2>\
\
<P>\
These data were generated and analyzed in\
<A HREF="http://bioinformatics-renlab.ucsd.edu/rentrac/" TARGET=_BLANK>Bing Ren&#39;s laboratory</A>\
at the Ludwig Institute for Cancer Research.\
</P>\
<P>\
Contact: <A HREF="mailto:&#121;&#55;&#115;h&#101;n&#64;&#117;&#99;&#115;&#100;.\
&#101;&#100;u">Yin Shen</A>\
<!-- above address is y7shen at ucsd.edu -->\
</P>\
\
<H2>References</H2>\
\
<p>\
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.\
<a href="https://www.nature.com/articles/nmeth.1226" target="_blank">\
Mapping and quantifying mammalian transcriptomes by RNA-Seq</a>.\
<em>Nat Methods</em>. 2008 Jul;5(7):621-8.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18516045" target="_blank">18516045</a>\
</p>\
\
<p>\
Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A.\
<a href="https://academic.oup.com/nar/article/37/18/e123/1085684" target="_blank">\
Transcriptome analysis by strand-specific sequencing of complementary DNA</a>.\
<em>Nucleic Acids Res</em>. 2009 Oct;37(18):e123.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19620212" target="_blank">19620212</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764448/" target="_blank">PMC2764448</a>\
</p>\
\
<p>\
Trapnell C, Pachter L, Salzberg SL.\
<a href="https://academic.oup.com/bioinformatics/article/25/9/1105/203994" target="_blank">\
TopHat: discovering splice junctions with RNA-Seq</a>.\
<em>Bioinformatics</em>. 2009 May 1;25(9):1105-11.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19289445" target="_blank">19289445</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672628/" target="_blank">PMC2672628</a>\
</p>\
\
<p>\
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter\
L.\
<a href="https://www.nature.com/articles/nbt.1621" target="_blank">\
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform\
switching during cell differentiation</a>.\
<em>Nat Biotechnol</em>. 2010 May;28(5):511-5.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20436464" target="_blank">20436464</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146043/" target="_blank">PMC3146043</a>\
</p>\
\
<H2>Data Release Policy</H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column, above.  The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
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wgEncodeLicrTfbs	LICR TFBS	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR	0	100	0	0	0	127	127	127	0	0	0			\
<H2> Description </H2>\
\
<P>\
This track shows a comprehensive survey of <i>cis</i>-regulatory elements\
in the mouse genome by using ChIP-seq &#40;Robertson <EM> et al.</EM>, 2007&#41; to identify\
transcription factor binding sites (TFBS) and chromatin modification\
profiles in various mouse &#40;C57BL/6&#41; tissues, primary cells, and cell lines. \
</P> \
<P>\
The Ren lab examined RNA polymerase II &#40;PolII&#41;, \
co-activator protein p300, the insulator protein CTCF, and \
the following chromatin modification marks: H3K4me3 and H3K4me1, \
H3K27ac, H3K36me3, H3K9me3, and H3K27me3 due to their \
demonstrated utilities in identifying promoters, enhancers, \
insulator elements, actively transcribed gene bodies, and \
silent chromatin regions &#40;Barski <EM>et al.</EM>, 2007; Bernstein <EM>et al.</EM>, 2006; Blow <EM>et al.</EM>, 2010; \
Creyghton <EM>et al.</EM>, 2010; Francis <EM>et al.</EM>, 2004; Hawkins <EM>et al.</EM>, 2011; Heintzman <EM>et al.</EM>, 2009; Kim <EM>et al.</EM>, 2007; Kim <EM> et al.</EM>, 2005; Krogan <EM>et al.</EM>, 2003; Li <EM>et al.</EM>, 2002; Peters <EM> et al.</EM>, 2001; Rada-Iglesias <EM>et al.</EM>, 2011; Schotta <EM>et al.</EM>, 2002; Visel <EM>et al.</EM>, 2009&#41;.\
Enrichment of PolII signals is a strong indicator of \
an active promoter and the presence of p300 outside of\
promoter regions has been used as a mark for enhancers.  \
CTCF binding sites are considered as a mark for \
potential insulator elements.  H3K4me3 is an active mark \
for promoters and H3K27ac is an active mark for both promoters \
and enhancers.  In the absence of H3K4me3, H3K4me1 serves as an\
active mark for enhancers.  H3K36me3 is normally found in actively \
transcribed gene bodies whereas both H3K9me3 and H3K27me3 are common\
repressive marks for transcriptionally silent chromatin regions.\
For each transcription factor or chromatin mark in each tissue, \
ChIP-seq was carried out with at least two biological \
replicates. Each experiment produced 20-30 million uniquely-mapped monoclonal tags.\
</P>\
\
<H2> Display Conventions and Configuration </H2>\
<P>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
<DL>\
<DT><I>Peaks</I></DT><DD> Regions of signal enrichment based on processed data\
(normalized data from pooled replicates). Intensity is represented in\
grayscale; darker shading shows higher intensity (a solid vertical line\
\	in the peak region represents the point with the highest signal).\
</DD>\
<DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based on\
processed data.</DD>\
</DL>\
</P>\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
<P>\
<!--echo var="BROWSER_HOST" -->\
Additional views are available on the Downloads page. \
</P>\
\
<H2> Methods </H2>\
<P>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
</P>\
\
<P><DT><B><I>Enrichment and Library Preparation</I></B></DT>\
\
Chromatin immunoprecipitation was performed according to the <A HREF="http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" \
TARGET=_BLANK>Ren Lab ChIP Protocol</A>.\
</P>\
<P>\
Library construction was performed according to the <A HREF="http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf"\
TARGET=_BLANK>Ren Lab Library Protocol</A>.\
</P>\
\
<P><DT><B><I>Sequencing and Analysis</I></B></DT>\
Samples were sequenced on Illumina Genome Analyzer II,\
Genome Analyzer IIx and HiSeq 2000 platforms\
for 36 cycles.  Image analysis, base calling and \
alignment to the mouse genome version NCBI37/mm9 were performed \
using Illumina&#39;s RTA and Genome Analyzer Pipeline software. \
Alignment to the mouse genome was performed using ELAND or\
<a href="http://bowtie-bio.sourceforge.net/index.shtml" target="_blank">Bowtie</a>\
(Langmead <EM>et al.</EM>, 2009) with \
a seed length of 25 and allowing up to two mismatches. \
Only the sequences that mapped to one location were used \
for further analysis.  Of those sequences, clonal reads,\
defined as having the same start position on the same \
strand, were discarded.  BED and wig files were\
created using custom perl scripts.\
</P>\
\
<h2>Release Notes</h2>\
\
<p>\
This is Release 3 (August 2012). It contains a total of 58 ChIP-seq experiments on transcription factor binding.  In this release, four controls (inputs) were dropped because they did not have accompanying TFBS experiments.\
</p>\
<p>\
An error surrounding the metadata designation of replicates of the fastq and alignment files of Kidney PolII datasets has been fixed.\
</p>\
\
<H2> Credits </H2>\
\
<P>\
These data were generated and analyzed in\
<A HREF="http://renlab.sdsc.edu/renlab_website/" TARGET=_BLANK>Bing Ren&#39;s laboratory</A>\
at the Ludwig Institute for Cancer Research (LICR).\
</P>\
<P>\
Contact: <A HREF="mailto:&#121;&#55;&#115;h&#101;n&#64;&#117;&#99;&#115;&#100;.\
&#101;&#100;u">Yin Shen</A>\
<!-- above address is y7shen at ucsd.edu -->\
</P>\
\
\
<H2> References </H2>\
<p>\
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17512414"\
target="_blank">\
High-resolution profiling of histone methylations in the human genome</a>.\
<em>Cell</em>. 2007 May 18;129(4):823-37.\
</p>\
<p>\
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/16630819"\
target="_blank">\
A bivalent chromatin structure marks key developmental genes in embryonic stem cells</a>.\
<em>Cell</em>. 2006 Apr 21;125(2):315-26.\
</p>\
<p>\
Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20729851"\
target="_blank">\
ChIP-Seq identification of weakly conserved heart enhancers</a>.\
<em>Nat Genet</em>. 2010 Sep;42(9):806-10.\
</p>\
<p>\
Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21106759"\
target="_blank">\
Histone H3K27ac separates active from poised enhancers and predicts developmental state</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2010 Dec 14;107(50):21931-6.\
</p>\
<p>\
Francis NJ, Kingston RE, Woodcock CL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/15567868"\
target="_blank">\
Chromatin compaction by a polycomb group protein complex</a>.\
<em>Science</em>. 2004 Nov 26;306(5701):1574-7.\
</p>\
<p>\
Hawkins RD, Hon GC, Yang C, Antosiewicz-Bourget JE, Lee LK, Ngo QM, Klugman S, Ching KA, Edsall LE, Ye Z <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21876557"\
target="_blank">\
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency</a>.\
<em>Cell Res</em>. 2011 Oct;21(10):1393-409.\
</p>\
<p>\
Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19295514"\
target="_blank">\
Histone modifications at human enhancers reflect global cell-type-specific gene expression</a>.\
<em>Nature</em>. 2009 May 7;459(7243):108-12.\
</p>\
<p>\
Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17382889"\
target="_blank">\
Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome</a>.\
<em>Cell</em>. 2007 Mar 23;128(6):1231-45.\
</p>\
<p>\
Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/15899964"\
target="_blank">\
Direct isolation and identification of promoters in the human genome</a>.\
<em>Genome Res</em>. 2005 Jun;15(6):830-9.\
</p>\
<p>\
Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/12773564"\
target="_blank">\
Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II</a>.\
<em>Mol Cell Biol</em>. 2003 Jun;23(12):4207-18.\
</p>\
<p>\
Langmead B, Trapnell C, Pop M, Salzberg SL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174"\
target="_blank">\
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>.\
<em>Genome Biol</em>. 2009;10(3):R25.\
</p>\
<p>\
Li J, Moazed D, Gygi SP.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/12381723"\
target="_blank">\
Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation</a>.\
<em>J Biol Chem</em>. 2002 Dec 20;277(51):49383-8.\
</p>\
<p>\
Peters AH, O'Carroll D, Scherthan H, Mechtler K, Sauer S, Sch&#246;fer C, Weipoltshammer K, Pagani M, Lachner M, Kohlmaier A <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/11701123"\
target="_blank">\
Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability</a>.\
<em>Cell</em>. 2001 Nov 2;107(3):323-37.\
</p>\
<p>\
Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21160473"\
target="_blank">\
A unique chromatin signature uncovers early developmental enhancers in humans</a>.\
<em>Nature</em>. 2011 Feb 10;470(7333):279-83.\
</p>\
<p>\
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17558387"\
target="_blank">\
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing</a>.\
<em>Nat Methods</em>. 2007 Aug;4(8):651-7.\
</p>\
<p>\
Schotta G, Ebert A, Krauss V, Fischer A, Hoffmann J, Rea S, Jenuwein T, Dorn R, Reuter G.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/11867540"\
target="_blank">\
Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing</a>.\
<em>EMBO J</em>. 2002 Mar 1;21(5):1121-31.\
</p>\
<p>\
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19212405"\
target="_blank">\
ChIP-seq accurately predicts tissue-specific activity of enhancers</a>.\
<em>Nature</em>. 2009 Feb 12;457(7231):854-8.\
</p>\
\
\
<H2> Data Release Policy </H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column, above.  The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
\
\
\
\
\
	regulation	1	compositeTrack on\
controlledVocabulary encode/cv.ra cellType=cell factor=antibody sex=sex age=age strain=strain control=control\
dimensionAchecked A1DULT8WKS,IMMORTAL\
dimensions dimensionX=cellType dimensionY=factor dimensionA=age\
dragAndDrop subTracks\
fileSortOrder cell=Cell_Line antibody=Antibody<BR>Target sex=Sex age=Age replicate=Replicate view=View dccAccession=UCSC_Accession geoSampleAccession=GEO_Sample<BR>Accession fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until\
filterComposite dimensionA=multi\
group regulation\
html wgEncodeLicrTfbs.release3\
longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR\
noInherit on\
priority 0\
shortLabel LICR TFBS\
sortOrder cellType=+ factor=+ view=+ age=+\
subGroup1 view Views Peaks=Peaks Signal=Signal\
subGroup2 cellType Cell_Line  B1MARROW=Bone_Marrow B1MDM=Bone_Marrow_Derived_Macrophage CBELLUM=Cerebellum CORTEX=Cortex ESB4=ES-Bruce4 HEART=Heart KIDNEY=Kidney LIMB=Limb LIVER=Liver LUNG=Lung MEF=MEF MEL=MEL OLFACT=Olfactory_Bulb PLAC=Placenta SMINT=Small_Intestine SPLEEN=Spleen TESTIS=Testis THYMUS=Thymus WBRAIN=Whole_Brain\
subGroup3 factor Factor CTCF=CTCF P300=p300 POL2=Pol2 INPUT=Input\
subGroup4 sex Sex M=M F=F U=U\
subGroup5 age Age A1DULT8WKS=Adult_8_weeks A2DULT24WKS=adult_24_weeks E0=Embryonic_day_0 E14HALF=Embryonic_day_14.5 IMMORTAL=Immortal_cells\
subGroup6 strain Strain C57BL6=C57BL/6\
subGroup7 control Control STD=std\
track wgEncodeLicrTfbs\
type bed 3\
visibilityViewDefaults Peaks=dense Signal=full\

wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6SigRep1	Lung 8w S 1	bigWig 1.000000 672685.000000	Lung Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	100	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Lung 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=LUNG localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqLungCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 672685.000000\

ctgPos	Map Contigs	ctgPos	Physical Map Contigs	0	100	150	0	0	202	127	127	0	0	0			<H2>Description</H2>\
This track shows the locations of mouse contigs on the physical map. \
The underlying data are derived from NCBI information\
specific to this assembly. Although the  NCBI data indicates the \
orientations of the contigs based on how they were assembled into the final \
sequence, all contigs in this track are oriented to the &quot;+&quot; strand. \
\
	map	0	color 150,0,0\
group map\
longLabel Physical Map Contigs\
shortLabel Map Contigs\
track ctgPos\
type ctgPos\
visibility hide\

wgEncodeMapability	Mappability	bigWig 0.00 1.00	Mappability or Uniqueness of Reference Genome from ENCODE	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
These tracks display the level of sequence uniqueness of the reference mm9\
genome.  They were generated using different window sizes and high signal\
will be found in areas where the sequence is unique.\
\
\
<h2>Display Conventions and Configuration</h2>\
<p>\
This track contains multiple subtracks representing different cell types\
that display individually on the browser. Instructions for configuring tracks\
with multiple subtracks are\
<A HREF="/goldenPath/help/multiView.html" TARGET=_BLANK>here</A>.\
</p>\
<p>\
These tracks provide a measure of how often the sequence found at the particular\
location will align within the whole genome.  Unlike measures of uniqueness, alignability\
will tolerate up to 2 mismatches. These tracks are in the form of signals ranging from\
0 to 1 and have several configuration options.\
</p>\
\
<H2>Methods</H2>\
<P>\
The <em>CRG Alignability</em> tracks show how uniquely k-mer sequences align \
to a region of the genome. \
By using the <A HREF="http://gemlibrary.sourceforge.net" TARGET=_BLANK>GEM mapper aligner</a>, \
where up to two mismatches were allowed, the method is equivalent to mapping \
sliding windows of k-mers back to the genome (where k has been set to 36, 40, \
50, 75 or 100 nucleotides to produce these tracks).\
For each window, a mappability score was computed \
(S = 1/(number of matches found in the genome): S=1 means one match in the \
genome, S=0.5 is two matches in the genome, and so on). The \
<em>CRG Alignability</em> tracks were \
generated independently of the ENCODE project, in the framework of the GEM \
(GEnome Multitool) project.\
\
<h2>Release Notes</h2>\
<p>\
This is Release 1 (June 2012) of the ENCODE mappability track. It is a port of the old mappability track into the ENCODE format.\
There are no new datasets.\
</p>\
\
<H2>Credits</H2>\
<P>\
The <em>CRG Alignability</em> track was created by Thomas Derrien and\
<A HREF="mailto:&#112;&#97;&#111;l&#111;.\
&#114;&#105;&#98;&#101;&#99;&#97;&#64;&#103;&#109;&#97;&#105;l.\
&#99;o&#109;">Paolo Ribeca</A>\
<!-- above address is paolo.ribeca at gmail.com -->\
 in <A HREF="http://pasteur.crg.es/portal/page/portal/Internet/02_Research/01_Programmes/01_Bioinformatics_Genomics" \
TARGET=_BLANK>Roderic Guigo's lab</A> at the Centre for Genomic \
Regulation (CRG), Barcelona, Spain. TD was supported by funds from NHGRI \
for the ENCODE project, while PR was funded by a Consolider grant \
CDS2007-00050 from the Spanish Ministerio de Educaci&#243;n y Ciencia."\
</P>\
\
<h2>Data Release Policy</h2>\
Data users may freely use ENCODE data, but may not, without prior consent, \
submit publications that use an unpublished ENCODE dataset until nine months \
following the release of the dataset. This date is listed in the \
Restricted Until column, above. The full data release policy for ENCODE is available\
<a href="../ENCODE/terms.html" target=_blank>here</a>.\
	map	0	allButtonPair on\
autoScale off\
compositeTrack on\
dragAndDrop subTracks\
fileSortOrder grant=PI lab=Lab view=View size=Window_size dccAccession=UCSC_Accession fileSize=Size fileType=File_Type\
group map\
longLabel Mappability or Uniqueness of Reference Genome from ENCODE\
maxHeightPixels 100:32:16\
priority 0\
shortLabel Mappability\
sortOrder win=+ lab=+\
subGroup1 win Window_Size w036=36_bp w040=40_bp w050=50_bp w075=75_bp w100=100_bp\
subGroup2 lab Lab CRG=CRG-Guigo\
track wgEncodeMapability\
type bigWig 0.00 1.00\
viewLimits 0:1\
visibility hide\
windowingFunction mean+whiskers\

wgEncodeSydhTfbsMelMafkDm2p5dStdPk	MEL MafK_a	narrowPeak	MEL MafK (ab50322) DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	100	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL MafK (ab50322) DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL MafK_a\
subGroups view=Peaks factor=MAFKAB50322 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhTfbsMelMafkDm2p5dStdPk\
type narrowPeak\

mgcFullMrna	MGC Genes	psl	Mammalian Gene Collection Full ORF mRNAs	0	100	0	100	0	127	177	127	0	0	0			<h2>Description</h2>\
\
<p>\
This track shows alignments of mouse mRNAs from the\
<a href="https://genecollections.nci.nih.gov/MGC/" target="_blank">Mammalian Gene Collection</a>\
(MGC) having full-length open reading frames (ORFs) to the genome.\
The goal of the Mammalian Gene Collection is to provide researchers with\
unrestricted access to sequence-validated full-length protein-coding cDNA\
clones for human, mouse, and rat genes.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
The track follows the display conventions for\
<a href="/goldenPath/help/hgTracksHelp.html#GeneDisplay" target="_blank">gene prediction\
tracks</a>.\
</p>\
\
<p>\
An optional codon coloring feature is available for quick\
validation and comparison of gene predictions.\
To display codon colors, select the <em>genomic codons</em> option from the\
<em>Color track by codons</em> pull-down menu. For more information\
about this feature, go to the\
<a href="/goldenPath/help/hgCodonColoring.html" target="_blank">\
Coloring Gene Predictions and Annotations by Codon</a> page.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
GenBank mouse MGC mRNAs identified as having full-length ORFs\
were aligned against the genome using blat. When a single mRNA\
aligned in multiple places, the alignment having the highest base identity was\
found.  Only alignments having a base identity level within 1% of\
the best and at least 95% base identity with the genomic sequence\
were kept.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
The mouse MGC full-length mRNA track was produced at UCSC from\
mRNA sequence data submitted to\
<a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">\
GenBank</a> by the Mammalian Gene Collection project.\
</p>\
\
<h2>References</h2>\
\
<p>\
Mammalian Gene Collection project\
<a href="https://genecollections.nci.nih.gov/MGC/Info/References" target="_blank">references</a>.\
</p>\
\
<p>\
Kent WJ.\
<a href="https://genome.cshlp.org/content/12/4/656.full" target="_blank">\
BLAT--the BLAST-like alignment tool</a>.\
<em>Genome Res</em>. 2002 Apr;12(4):656-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a>\
</p>\
	genes	1	baseColorDefault diffCodons\
baseColorUseCds genbank\
baseColorUseSequence genbank\
color 0,100,0\
group genes\
indelDoubleInsert on\
indelQueryInsert on\
longLabel Mammalian Gene Collection Full ORF mRNAs\
shortLabel MGC Genes\
showCdsAllScales .\
showCdsMaxZoom 10000.0\
showDiffBasesAllScales .\
showDiffBasesMaxZoom 10000.0\
track mgcFullMrna\
type psl\
visibility hide\

jaxAllele	MGI Allele	bed 12 +	Jackson Laboratory / Mouse Genome Informatics Allele	0	100	200	0	110	200	0	110	0	0	0		http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&id=$$	<H2>Description</H2>\
<P>\
This track shows \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>Mouse Genome \
Informatics (MGI)</A>\
representative transcripts associated with \
MGI-curated alleles.  Items are named by concatenating the\
representative transcript ID and allele symbol. \
All chemical- and radiation-induced alleles have been\
combined as type &quot;Induced.&quot; \
Floxed/Frt, reporter, knock-out and knock-in\
targeted alleles are combined as type &quot;Targeted.&quot; \
Random-expressed, random-gene\
disruption, and Cre/Flp transgenes are combined as\
type &quot;Transgenic&quot;. \
The other types included in this track are &quot;GeneTrapped&quot;, \
&quot;Spontaneous&quot; and &quot;Other&quot;.\
</P>\
\
<H2>Methods</H2>\
<P>\
The MGI database report \
<A HREF="ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt"\
TARGET=_BLANK>MGI_PhenotypicAllele.rpt</A> was parsed to provide a\
list of all curated alleles that have associated representative \
transcripts.</P>\
\
<H2>Credits</H2>\
<P>\
Thanks to \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>MGI</A> \
at The Jackson Laboratory, \
and Bob Sinclair in particular, for providing these data.</P>\
\
	phenoAllele	1	altColor 200, 0, 110\
color 200, 0, 110\
group phenoAllele\
html jaxAlleleOld\
longLabel Jackson Laboratory / Mouse Genome Informatics Allele\
noScoreFilter .\
shortLabel MGI Allele\
track jaxAllele\
type bed 12 +\
url http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&id=$$\
urlLabel MGI Phenotypic Allele:\
visibility hide\

jaxGeneTrap	MGI Gene Trap	bed 12 +	Jackson Laboratory / Mouse Genome Informatics DNA and RNA Gene Traps	0	100	0	0	0	127	127	127	0	0	0		http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&id=$$	<H2>Description</H2>\
<P>\
This track shows gene trap sequence tags from GenBank \
<A HREF="https://www.ncbi.nlm.nih.gov/dbGSS/" TARGET=_BLANK>dbGSS</A>\
that have an RNA-based sequence tag method (5'-RACE or 3'-RACE) or\
DNA-based sequence tag method.  DNA-based gene trap sequence tags\
(purple) are derived from genomic DNA at the site of gene trap vector\
insertion.  RNA-based gene trap sequence tags are derived from the\
exon adjacent to the insertion site. If the sequence tag method is\
5'-RACE (blue), the insertion site is in the intron downstream from\
the most 3' exon represented in the sequence tag. If the sequence tag\
is 3'-RACE (green), the insertion site is in the intron upstream from\
the most 5' exon represented in the sequence tag.\
</P>\
<P>\
Gene trap mutagenesis requires that the vector inserts in the correct\
transcriptional orientation of the &quot;trapped&quot; gene. Sequence\
tags that overlap known genes in the opposite transcriptional\
orientation do not disrupt those genes from a gene trapping mechanism.\
</P>\
\
<H2>Methods</H2>\
<P>\
Sequence tags were collected from dbGSS and aligned to the reference \
genome by \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>Mouse Genome \
Informatics (MGI)</A> at The Jackson Laboratory.</P>\
\
<H2>Credits</H2>\
<P>\
Thanks to \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>MGI</A> \
at The Jackson Laboratory, \
and Bob Sinclair in particular, for providing these data.</P>\
	phenoAllele	1	group phenoAllele\
itemRgb on\
longLabel Jackson Laboratory / Mouse Genome Informatics DNA and RNA Gene Traps\
noScoreFilter .\
shortLabel MGI Gene Trap\
track jaxGeneTrap\
type bed 12 +\
url http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&id=$$\
urlLabel MGI Phenotypic Allele:\
visibility hide\

jaxPhenotype	MGI Phenotype	bed 12 +	Jackson Laboratory / Mouse Genome Informatics Phenotype	0	100	190	110	0	222	182	127	0	0	0		http://www.informatics.jax.org/searches/allele_report.cgi?markerID=$$	<H2>Description</H2>\
<P>\
This track shows \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>Mouse Genome \
Informatics</A> (MGI)\
representative transcripts associated with\
<A HREF="http://www.informatics.jax.org/vocab/mp_ontology/" \
TARGET=_BLANK>Mammalian Phenotype Ontology</A> Top-Level terms.\
The terms have been abbreviated for display as follows:\
<BR><BR>\
<TABLE>\
<TR><TD><B>Abbreviation</B></TD><TD><B>MPO Term</B></TD></TR>\
<TR><TD>Adipose</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005375"\
           TARGET=_BLANK>adipose tissue phenotype</A></TD></TR>\
<TR><TD>Behavior</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005386"\
           TARGET=_BLANK>behavior/neurological phenotype</A></TD></TR>\
<TR><TD>Cardiovascular</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005385"\
           TARGET=_BLANK>cardiovascular system phenotype</A></TD></TR>\
<TR><TD>Cellular</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005384"\
           TARGET=_BLANK>cellular phenotype</A></TD></TR>\
<TR><TD>Craniofacial</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005382"\
           TARGET=_BLANK>craniofacial phenotype</A></TD></TR>\
<TR><TD>Digestive</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005381"\
           TARGET=_BLANK>digestive/alimentary phenotype</A></TD></TR>\
<TR><TD>Embryogenesis</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005380"\
           TARGET=_BLANK>embryogenesis phenotype</A></TD></TR>\
<TR><TD>Embryonic Lethal</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0010768"\
           TARGET=_BLANK>lethality-embryonic perinatal</A></TD></TR>\
<TR><TD>Gland</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005379"\
           TARGET=_BLANK>endocrine/exocrine gland phenotype</A></TD></TR>\
<TR><TD>Growth Size</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005378"\
           TARGET=_BLANK>growth/size phenotype</A></TD></TR>\
<TR><TD>Hearing/Ear</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005377"\
           TARGET=_BLANK>hearing/vestibular/ear phenotype</A></TD></TR>\
<TR><TD>Hematopoietic</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005397"\
           TARGET=_BLANK>hematopoietic system phenotype</A></TD></TR>\
<TR><TD>Homeostasis</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005376"\
           TARGET=_BLANK>homeostasis/metabolism phenotype</A></TD></TR>\
<TR><TD>Immune</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005387"\
           TARGET=_BLANK>immune system phenotype</A></TD></TR>\
<TR><TD>Integument</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0010771"\
           TARGET=_BLANK>integument phenotype</A></TD></TR>\
<TR><TD>Life Span</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0010768"\
           TARGET=_BLANK>life span-post-weaning/aging</A></TD></TR>\
<TR><TD>Limbs and Tail</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005371"\
           TARGET=_BLANK>limbs/digits/tail phenotype</A></TD></TR>\
<TR><TD>Liver and Bile</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005370"\
           TARGET=_BLANK>liver/biliary system phenotype</A></TD></TR>\
<TR><TD>Mortality</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0010768"\
           TARGET=_BLANK>mortality/aging</A></TD></TR>\
<TR><TD>Muscle</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005369"\
           TARGET=_BLANK>muscle phenotype</A></TD></TR>\
<TR><TD>Nervous System</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0003631"\
           TARGET=_BLANK>nervous system phenotype</A></TD></TR>\
<TR><TD>Pigmentation</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0001186"\
           TARGET=_BLANK>pigmentation phenotype</A></TD></TR>\
<TR><TD>Postnatal Lethal</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0010768"\
           TARGET=_BLANK>lethality-postnatal</A></TD></TR>\
<TR><TD>Renal/Urinary</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005367"\
           TARGET=_BLANK>renal/urinary system phenotype</A></TD></TR>\
<TR><TD>Reproductive</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005389"\
           TARGET=_BLANK>reproductive system phenotype</A></TD></TR>\
<TR><TD>Respiratory</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005388"\
           TARGET=_BLANK>respiratory system phenotype</A></TD></TR>\
<TR><TD>Skeleton</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005390"\
           TARGET=_BLANK>skeleton phenotype</A></TD></TR>\
<TR><TD>Skin/Coat/Nails</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0010771"\
           TARGET=_BLANK>skin/coat/nails phenotype</A></TD></TR>\
<TR><TD>Taste/Smell</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005394"\
           TARGET=_BLANK>taste/olfaction phenotype</A></TD></TR>\
<TR><TD>Touch</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0010771"\
           TARGET=_BLANK>touch/vibrissae phenotype</A></TD></TR>\
<TR><TD>Tumorigenesis</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0002006"\
           TARGET=_BLANK>tumorigenesis</A></TD></TR>\
<TR><TD>Vision/Eye</TD>\
    <TD><A HREF="http://www.informatics.jax.org/vocab/mp_ontology/MP:0005391"\
           TARGET=_BLANK>vision/eye phenotype</A></TD></TR>\
</TABLE></P>\
\
<H2>Methods</H2>\
<P>\
The MGI database report \
<A HREF="ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt"\
TARGET=_BLANK>MGI_PhenotypicAllele.rpt</A> was parsed for\
markers and alleles that are associated with representative\
transcripts, and the Top-Level Mammalian Phenotype (MP) terms were\
captured. Note that these top-level terms can be associated with a\
marker multiple times (i.e. via multiple alleles). </P>\
\
<H2>Credits</H2>\
<P>\
Thanks to \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>MGI</A> \
at The Jackson Laboratory, \
and Bob Sinclair in particular, for providing these data.</P>\
\
	phenoAllele	1	color 190,110,0\
group phenoAllele\
longLabel Jackson Laboratory / Mouse Genome Informatics Phenotype\
noScoreFilter .\
shortLabel MGI Phenotype\
track jaxPhenotype\
type bed 12 +\
url http://www.informatics.jax.org/searches/allele_report.cgi?markerID=$$\
urlLabel MGI Phenotypic Allele(s):\
visibility hide\

jaxQtl	MGI QTL	bed 6 +	Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics	0	100	200	100	0	227	177	127	0	0	0		http://www.informatics.jax.org/marker/$$	<H2> Description </H2>\
<P>\
This track shows approximate positions of quantitative trait loci \
based on reported peak LOD scores from\
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>\
Mouse Genome Informatics</A> (MGI) at the \
<A HREF="https://www.jax.org/" TARGET=_BLANK>Jackson Laboratory</A>.\
</P>\
<H2>Credits</H2>\
<P>\
Thanks to \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>MGI</A> \
at the Jackson Laboratory, \
and Bob Sinclair in particular, for providing these data.</P>\
</P>\
	map	1	color 200,100,0\
group map\
longLabel Quantitative Trait Loci From Jackson Laboratory / Mouse Genome Informatics\
noScoreFilter .\
shortLabel MGI QTL\
track jaxQtl\
type bed 6 +\
url http://www.informatics.jax.org/marker/$$\
urlLabel MGI QTL Detail:\
visibility hide\

jaxRepTranscript	MGI RepTranscrpt	genePred	Jackson Laboratory / Mouse Genome Informatics Representative Transcript	0	100	0	0	150	127	127	202	0	0	0		http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=markerDetail&id=$$	<H2>Description</H2>\
<P>\
This track shows mappings of sequences chosen as &quot;best\
representative transcript&quot; for many highly curated \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>Mouse Genome \
Informatics</A> (MGI) genes.\
Representative transcript identifiers are a concatenation of the\
GenBank accession and the MGI gene symbol.</P>\
\
<H2>Methods</H2>\
<P>\
Representative transcript sequences were selected by \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>MGI</A>.\
The sequences were placed on the assembly using \
<A HREF="https://genome.cshlp.org/content/12/4/656.full" TARGET=_BLANK>Blat</A> \
and filtered to retain the single best hit.</P>\
\
<H2>Credits</H2>\
<P>\
Thanks to \
<A HREF="http://www.informatics.jax.org/" TARGET=_BLANK>MGI</A> \
at The Jackson Laboratory, \
and Bob Sinclair in particular, for providing these data.</P>\
\
	phenoAllele	1	baseColorUseCds none\
color 0,0,150\
group phenoAllele\
longLabel Jackson Laboratory / Mouse Genome Informatics Representative Transcript\
shortLabel MGI RepTranscrpt\
track jaxRepTranscript\
type genePred\
url http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=markerDetail&id=$$\
urlLabel MGI Gene Detail:\
visibility hide\

microsat	Microsatellite	bed 4	Microsatellites - Di-nucleotide and Tri-nucleotide Repeats	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track displays regions that are likely to be useful as microsatellite\
markers. These are sequences of at least 15 perfect di-nucleotide and \
tri-nucleotide repeats and tend to be highly polymorphic in the\
population.\
</P>\
\
<H2>Methods</H2>\
<P>\
The data shown in this track are a subset of the Simple Repeats track, \
selecting only those \
repeats of period 2 and 3, with 100% identity and no indels and with\
at least 15 copies of the repeat.  The Simple Repeats track is\
created using the <A HREF="https://tandem.bu.edu/trf/trf.submit.options.html" TARGET=_blank>\
Tandem Repeats Finder</A>.  For more information about this \
program, see Benson (1999).</P>\
\
<H2>Credits</H2>\
<P>\
Tandem Repeats Finder was written by \
<A HREF="https://tandem.bu.edu/benson.html" TARGET=_blank>Gary Benson</A>.</P>\
\
<H2>References</H2>\
\
<p>\
Benson G.\
<a href="https://academic.oup.com/nar/article/27/2/573/1061099/Tandem-repeats-finder-a-program-to-analyze-DNA" target="_blank">\
Tandem repeats finder: a program to analyze DNA sequences</a>.\
<em>Nucleic Acids Res</em>. 1999 Jan 15;27(2):573-80.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/9862982" target="_blank">9862982</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC148217/" target="_blank">PMC148217</a>\
</p>\
	varRep	1	group varRep\
longLabel Microsatellites - Di-nucleotide and Tri-nucleotide Repeats\
shortLabel Microsatellite\
track microsat\
type bed 4\
visibility hide\

wgEncodeCshlLongRnaSeqViewMinusRawSignal	Minus Raw Signal	bed 3	Long RNA-seq from ENCODE/Cold Spring Harbor Lab	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel Long RNA-seq from ENCODE/Cold Spring Harbor Lab\
maxHeightPixels 100:24:16\
minLimit 0\
parent wgEncodeCshlLongRnaSeq\
shortLabel Minus Raw Signal\
track wgEncodeCshlLongRnaSeqViewMinusRawSignal\
transformFunc NONE\
view MinusRawSignal\
viewLimits 1:10\
visibility full\
windowingFunction mean+whiskers\

wgEncodePsuRnaSeqViewMinusRawSignal	Minus Raw Signal	bed 3	RNA-seq from ENCODE/PSU	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
configurable on\
longLabel RNA-seq from ENCODE/PSU\
maxHeightPixels 100:50:16\
parent wgEncodePsuRnaSeq\
shortLabel Minus Raw Signal\
track wgEncodePsuRnaSeqViewMinusRawSignal\
transformFunc NONE\
view MinusRawSignal\
viewLimits -20000:-1\
visibility full\
windowingFunction mean+whiskers\

miRNA	miRNA	bed 6 .	MicroRNAs from miRBase	0	100	255	64	64	255	159	159	1	0	0		http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$	<H2>Description</H2>\
<P>\
The miRNA track shows microRNAs from\
<A HREF="https://www.mirbase.org/" TARGET="_blank">miRBase</A>.\
</P>\
\
<H2>Display Conventions and Configuration</H2>\
<P>\
The precursor forms of\
microRNAs (mirs) in the sense\
orientation are shown in black; those in the reverse orientation are colored\
grey.</P>\
<P>\
To display only those items that exceed a specific unnormalized score, enter\
a minimum score between 0 and 1000 in the text box at the top of the track \
description page. For this track, a score of 960 signifies that the miRNA is on the + strand and a\
score of 480 signifies that it is on the - strand.\
</P>\
\
<H2>Methods</H2>\
<P>\
Precursor miRNA genomic locations from\
<a href="https://www.mirbase.org/" target="_blank">miRBase</a>\
were calculated using wublastn for sequence alignment with the requirement of \
100% identity. The extents of the precursor sequences were not generally known,\
and were predicted based on base-paired hairpin structure. miRBase is \
described in Griffiths-Jones, S. <EM>et al</EM>. (2006). The miRNA Registry \
is described in Griffiths-Jones, S. (2004) and Weber, M.J. (2005) in the \
References section below.</p>\
\
<H2>Credits</H2>\
<P>\
Genome coordinates for this track were obtained from the miRBase sequences \
<A HREF="ftp://ftp.sanger.ac.uk/pub/mirbase/sequences/CURRENT/genomes/" \
TARGET=_BLANK>FTP site</A>.\
</P>\
\
<h2>References</h2>\
\
<p>\
When making use of these data, please cite the folowing articles in addition to\
the primary sources of the miRNA sequences:\
</p>\
\
<p>\
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.\
<a href="https://academic.oup.com/nar/article/36/suppl_1/D154/2507930" target="_blank">\
miRBase: tools for microRNA genomics</a>.\
<em>Nucleic Acids Res</em>. 2008 Jan 1;36(Database issue):D154-8.\
</p>\
\
<p>\
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ.\
<a href="https://academic.oup.com/nar/article/34/suppl_1/D140/1133563" target="_blank">\
miRBase: microRNA sequences, targets and gene nomenclature</a>.\
<em>Nucleic Acids Res</em>. 2006 Jan 1;34(Database issue):D140-4.\
</p>\
\
<p>\
Griffiths-Jones S.\
<a href="https://academic.oup.com/nar/article/32/suppl_1/D109/2505171" target="_blank">\
The microRNA Registry</a>.\
<em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D109-11.\
</p>\
\
<p>\
Weber MJ.\
<a href="https://febs.onlinelibrary.wiley.com/doi/abs/10.1111/j.1432-1033.2004.04389.x"\
target="_blank">New human and mouse microRNA genes found by homology search</a>.\
<em>Febs J</em>. 2005 Jan;272(1):59-73.\
</p>\
\
<p>\
The following publication provides guidelines on miRNA annotation:\
<br>Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X,\
Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M <em>et al</em>.\
<a href="https://rnajournal.cshlp.org/content/9/3/277.abstract" target="_blank">\
A uniform system for microRNA annotation</a>.\
<em>RNA</em>. 2003 Mar;9(3):277-9.\
</p>\
	genes	1	color 255,64,64\
dataVersion Release 13.0 (March 2009)\
group genes\
longLabel MicroRNAs from miRBase\
shortLabel miRNA\
track miRNA\
type bed 6 .\
url http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$\
urlLabel miRBase:\
useScore 1\
visibility hide\

multiz30way	Multiz Align	wigMaf 0.0 1.0	Multiz Alignments of 30 Vertebrates	3	100	0	10	100	0	90	10	0	0	0			<H2>Description</H2>\
<P>\
This track shows multiple alignments of 30 vertebrate\
species and three measures of evolutionary conservation --\
conservation across all 30 species, an alternative \
measurement restricted to the euarchontoglires subset\
(10 species plus mouse) of the alignment, and a\
measurement restricted to the placental mammal subset \
(19 species plus mouse) of the alignment.\
These three measurements produce the same results in \
regions where only euarchontoglires appear in the alignment. \
For other regions, the non-euarchontoglires species can either \
boost the scores (if conserved) or decrease them (if non-conserved).\
The placental mammal conservation helps to identify sequences that are under \
different evolutionary pressures in mammals and non-mammal vertebrates.\
</P>\
<P>\
<UL>\
<LI> Euarchontoglire subset: mouse(mm9), rat(rn4), Guinea Pig(cavPor2),\
Rabbit(oryCun1), Human(hg18), Chimp(panTro2), Orangutan(ponAbe2),\
Rhesus(rheMac2), Marmoset(calJac1), Bushbaby(otoGar1), Tree Shrew(tupBel1)\
<LI> Placental mammal subset: the euarchontoglires above plus:\
Shrew(sorAra1), Hedgehog(eriEur1), Dog(canFam2), Cat(felCat3),\
Horse(equCab1), Cow(bosTau3), Armadillo(dasNov1), Elephant(loxAfr1),\
Tenrec(echTel1)\
<LI> Vertebrates: the placentals and euarchontoglires above plus:\
Opossum(monDom4), Platypus(ornAna1), Chicken(galGal3), Lizard(anoCar1),\
Frog(xenTro2), Tetraodon(tetNig1), Fugu(fr2), Stickleback(gasAcu1),\
Medaka(oryLat1), Zebrafish(danRer5)\
</UL>\
</P>\
<P>\
The multiple alignments were generated using multiz and \
other tools in the UCSC/<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Penn State Bioinformatics</A>\
comparative genomics alignment pipeline.\
The conservation measurements were created using the phastCons package from\
<A HREF="http://siepellab.labsites.cshl.edu/" TARGET=_blank>\
Adam Siepel</A> at Cold Spring Harbor Laboratory. </P>\
<P>\
Details of the alignment parameters are noted in the genomewiki\
<A HREF="http://genomewiki.ucsc.edu/index.php/Mm9_multiple_alignment"\
TARGET=_blank>Mm9 multiple alignment</A> page.\
</P>\
<P>\
The species aligned for this track include the reptile, amphibian, \
bird, and fish clades, as well as marsupial, monotreme (platypus), \
and placental mammals. Compared to the previous 17-vertebrate alignment,\
this track includes 13 new species and 4 species with updated\
sequence assemblies (<B>Table 1</B>). The new species consist of seven \
high-coverage (5-8.5X) assemblies (orangutan, marmoset, horse, platypus, \
lizard, and two teleost fish: stickleback and medaka)\
and six low-coverage (2X) genome assemblies from mammalian species selected for \
sampling by NHGRI (bushbaby, tree shrew, guinea pig, \
hedgehog, common shrew, and cat).\
The cow, chicken, fugu, and zebrafish assemblies in this \
track have been updated from those used in the previous 17-species alignment.\
</P>\
<P>\
UCSC has repeatmasked and aligned the low-coverage genome assemblies, and\
provides the sequence for download; however, we do not construct\
genome browsers for them. Missing sequence in the low-coverage assemblies is\
highlighted in the track display by regions of yellow when zoomed out\
and Ns displayed at base level (see <EM>Gap Annotation</EM>, below). </P>\
<P>\
<BLOCKQUOTE><TABLE BORDER=1 CELLPADDING=4 BORDERCOLOR="#aaaaaa">\
<TR ALIGN=left><TH>Organism</TH><TH>Species</TH><TH>Release date</TH><TH>UCSC version</TH></TR>\
<TR ALIGN=left><TD>Mouse</TD><TD>Mus musculus</TD><TD>\
    Jul 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=mm9"\
    TARGET=_blank>mm9</A></TD></TR>\
<TR ALIGN=left><TD>Armadillo</TD><TD>Dasypus novemcinctus</TD><TD>May 2005</TD>\
    <TD> dasNov1</TD></TR>\
<TR ALIGN=left><TD>Bushbaby</TD><TD>Otolemur garnetti</TD><TD>Dec 2006</TD>\
    <TD> otoGar1</TD></TR>\
<TR ALIGN=left><TD>Cat</TD><TD>Felis catus</TD><TD>\
    Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=felCat3"\
    TARGET=_blank>felCat3</A></TD></TR>\
<TR ALIGN=left><TD>Chicken</TD><TD>Gallus gallus</TD><TD>\
    May 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=galGal3"\
    TARGET=_blank>galGal3</A></TD></TR>\
<TR ALIGN=left><TD>Chimpanzee</TD><TD>Pan troglodytes</TD><TD>\
    Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=panTro2"\
    TARGET=_blank>panTro2</A></TD></TR>\
<TR ALIGN=left><TD>Cow</TD><TD>Bos taurus</TD><TD>\
    Aug 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=bosTau3"\
    TARGET=_blank>bosTau3</A></TD></TR>\
<TR ALIGN=left><TD>Dog</TD><TD>Canis familiaris</TD><TD>\
    May 2005</TD><TD> <A HREF="../cgi-bin/hgGateway?db=canFam2"\
    TARGET=_blank>canFam2</A></TD></TR>\
<TR ALIGN=left><TD>Elephant</TD><TD>Loxodonta africana</TD><TD>May 2005</TD>\
    <TD> loxAfr1</TD></TR>\
<TR ALIGN=left><TD>Frog</TD><TD>Xenopus tropicalis</TD><TD>\
    Aug 2005</TD><TD> <A HREF="../cgi-bin/hgGateway?db=xenTro2"\
    TARGET=_blank>xenTro2</A></TD></TR>\
<TR ALIGN=left><TD>Fugu</TD><TD>Takifugu rubripes</TD><TD>\
    Oct 2004</TD><TD> <A HREF="../cgi-bin/hgGateway?db=fr2"\
    TARGET=_blank>fr2</A></TD></TR>\
<TR ALIGN=left><TD>Guinea pig</TD><TD>Cavia porcellus</TD><TD>Oct 2005</TD>\
    <TD> cavPor2</TD></TR>\
<TR ALIGN=left><TD>Hedgehog</TD><TD>Erinaceus europaeus</TD><TD>June 2006</TD>\
    <TD> eriEur1</TD></TR>\
<TR ALIGN=left><TD>Horse</TD><TD>Equus caballus</TD><TD>\
    Jan 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=equCab1"\
    TARGET=_blank>equCab1</A></TD></TR>\
<TR ALIGN=left><TD>Human</TD><TD>Homo sapiens</TD><TD>\
    Mar 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=hg18"\
    TARGET=_blank>hg18</A></TD></TR>\
<TR ALIGN=left><TD>Lizard</TD><TD>Anolis carolinensis</TD><TD>\
    Feb 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=anoCar1"\
    TARGET=_blank>anoCar1</A></TD></TR>\
<TR ALIGN=left><TD>Marmoset</TD><TD>Callithrix jacchus</TD><TD>June 2007</TD>\
    <TD>calJac1</TD></TR>\
<TR ALIGN=left><TD>Medaka</TD><TD>Oryzias latipes</TD><TD>\
    Apr 2006</TD><TD>oryLat1</A></TD></TR>\
<TR ALIGN=left><TD>Opossum</TD><TD>Monodelphis domestica</TD><TD>\
    Jan 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=monDom4"\
    TARGET=_blank>monDom4</A></TD></TR>\
<TR ALIGN=left><TD>Orangutan</TD><TD>Pongo pygmaeus abelii</TD><TD>\
    July 2007</TD><TD>ponAbe2</TD></TR>\
<TR ALIGN=left><TD>Platypus</TD><TD>Ornithorhychus anatinus</TD><TD>\
    Mar 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=ornAna1"\
    TARGET=_blank>ornAna1</A></TD></TR>\
<TR ALIGN=left><TD>Rabbit</TD><TD>Oryctolagus cuniculus</TD><TD>May 2005</TD>\
    <TD> oryCun1</TD></TR>\
<TR ALIGN=left><TD>Rat</TD><TD>Rattus norvegicus</TD><TD>\
    Nov 2004</TD><TD> <A HREF="../cgi-bin/hgGateway?db=rn4"\
    TARGET=_blank>rn4</A></TD></TR>\
<TR ALIGN=left><TD>Rhesus</TD><TD>Macaca mulatta</TD><TD>\
    Jan 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=rheMac2"\
    TARGET=_blank>rheMac2</A></TD></TR>\
<TR ALIGN=left><TD>Shrew</TD><TD>Sorex araneus</TD><TD>June 2006</TD>\
    <TD> sorAra1</TD></TR>\
<TR ALIGN=left><TD>Stickleback</TD><TD>Gasterosteus aculeatus</TD><TD>\
    Feb 2006</TD><TD> <A HREF="../cgi-bin/hgGateway?db=gasAcu1"\
    TARGET=_blank>gasAcu1</A></TD></TR>\
<TR ALIGN=left><TD>Tenrec</TD><TD>Echinops telfairi</TD><TD>July 2005</TD>\
    <TD> echTel1</TD></TR>\
<TR ALIGN=left><TD>Tetraodon</TD><TD>Tetraodon nigroviridis</TD><TD>\
    Feb 2004</TD><TD> <A HREF="../cgi-bin/hgGateway?db=tetNig1"\
    TARGET=_blank>tetNig1</A></TD></TR>\
<TR ALIGN=left><TD>Tree shrew</TD><TD>Tupaia belangeri</TD><TD>Dec 2006</TD>\
    <TD> tupBel1</TD></TR>\
<TR ALIGN=left><TD>Zebrafish</TD><TD>Danio rerio</TD><TD>\
    July 2007</TD><TD> <A HREF="../cgi-bin/hgGateway?db=danRer5"\
    TARGET=_blank>danRer5</A></TD></TR>\
</TABLE><BR>\
<B>Table 1.</B> <EM>Genome assemblies included in the 30-way Conservation \
track.</EM>\
</BLOCKQUOTE></P>\
\
<H2>Display Conventions and Configuration</H2>\
<P>\
The track configuration options allow the user to display either\
the vertebrate or placental mammal conservation scores, or both\
simultaneously.\
In full and pack display modes, conservation scores are displayed as a\
<EM>wiggle track</EM> (histogram) in which the height reflects the \
size of the score. \
The conservation wiggles can be configured in a variety of ways to \
highlight different aspects of the displayed information. \
Click the <A HREF="../goldenPath/help/hgWiggleTrackHelp.html" \
TARGET=_blank>Graph configuration help</A> link for an explanation \
of the configuration options.</P>\
<P>\
Pairwise alignments of each species to the mouse genome are \
displayed below the conservation histogram as a grayscale density plot (in \
pack mode) or as a wiggle (in full mode) that indicates alignment quality.\
In dense display mode, conservation is shown in grayscale using\
darker values to indicate higher levels of overall conservation \
as scored by phastCons. </P>\
<P>\
Checkboxes on the track configuration page allow selection of the\
species to include in the pairwise display.  \
Configuration buttons are available to select all of the species (<EM>Set \
all</EM>), deselect all of the species (<EM>Clear all</EM>), or \
use the default settings (<EM>Set defaults</EM>).\
By default, the following 8 species are included in the pairwise display:\
rat, human, orangutan, dog, horse, opossum, chicken, and stickleback.\
Note that excluding species from the pairwise display does not alter the\
the conservation score display.</P>\
<P>\
To view detailed information about the alignments at a specific\
position, zoom the display in to 30,000 or fewer bases, then click on\
the alignment.</P>\
\
<H3>Gap Annotation</H3>\
<P>\
The <EM>Display chains between alignments</EM> configuration option \
enables display of gaps between alignment blocks in the pairwise alignments in \
a manner similar to the Chain track display.  The following\
conventions are used:\
<UL>\
<LI><B>Single line:</B> no bases in the aligned species. Possibly due to a\
lineage-specific insertion between the aligned blocks in the mouse genome\
or a lineage-specific deletion between the aligned blocks in the aligning\
species.\
<LI><B>Double line:</B> aligning species has one or more unalignable bases in\
the gap region. Possibly due to excessive evolutionary distance between \
species or independent indels in the region between the aligned blocks in both\
species. \
<LI><B>Pale yellow coloring:</B> aligning species has Ns in the gap region.\
Reflects uncertainty in the relationship between the DNA of both species, due\
to lack of sequence in relevant portions of the aligning species. \
</UL></P>\
\
<H3>Genomic Breaks</H3>\
<P>\
Discontinuities in the genomic context (chromosome, scaffold or region) of the\
aligned DNA in the aligning species are shown as follows: \
<UL>\
<LI>\
<B>Vertical blue bar:</B> represents a discontinuity that persists indefinitely\
on either side, <em>e.g.</em> a large region of DNA on either side of the bar\
comes from a different chromosome in the aligned species due to a large scale\
rearrangement. \
<LI>\
<B>Green square brackets:</B> enclose shorter alignments consisting of DNA from\
one genomic context in the aligned species nested inside a larger chain of\
alignments from a different genomic context. The alignment within the\
brackets may represent a short misalignment, a lineage-specific insertion of a\
transposon in the mouse genome that aligns to a paralogous copy somewhere\
else in the aligned species, or other similar occurrence.\
</UL></P>\
\
<H3>Base Level</H3>\
<P>\
When zoomed-in to the base-level display, the track shows the base \
composition of each alignment. \
The numbers and symbols on the Gaps\
line indicate the lengths of gaps in the mouse sequence at those \
alignment positions relative to the longest non-mouse sequence. \
If there is sufficient space in the display, the size of the gap is shown. \
If the space is insufficient and the gap size is a multiple of 3, a \
&quot;*&quot; is displayed; other gap sizes are indicated by &quot;+&quot;.</P>\
<P>\
Codon translation is available in base-level display mode if the\
displayed region is identified as a coding segment. To display this annotation,\
select the species for translation from the pull-down menu in the Codon\
Translation configuration section at the top of the page. Then, select one of\
the following modes:\
<UL>\
<LI> \
<B>No codon translation:</B> the gene annotation is not used; the bases are\
displayed without translation. \
<LI>\
<B>Use default species reading frames for translation:</B> the annotations from the genome\
displayed \
in the <EM>Default species for translation</EM>; pull-down menu are used to\
translate all the aligned species present in the alignment. \
<LI>\
<B>Use reading frames for species if available, otherwise no translation:</B> codon\
translation is performed only for those species where the region is\
annotated as protein coding.\
<LI><B>Use reading frames for species if available, otherwise use default species:</B>\
codon translation is done on those species that are annotated as being protein\
coding over the aligned region using species-specific annotation; the remaining\
species are translated using the default species annotation. \
</UL></P>\
<P>\
Codon translation uses the following gene tracks as the basis for\
translation, depending on the species chosen (<B>Table 2</B>).  \
Species listed in the row labeled &quot;None&quot; do not have \
species-specific reading frames for gene translation.\
\
<BLOCKQUOTE><TABLE BORDER=1 CELLPADDING=4 BORDERCOLOR="#aaaaaa">\
<TR ALIGN=left><TD><B>Gene Track</B></TD><TD><B>Species</B></TD></TR>\
<TR ALIGN=left><TD>Known Genes</TD><TD>human, mouse</TD></TR>\
<TR ALIGN=left><TD>Ensembl Genes</TD><TD>rat, rhesus, chimp, dog, opossum, platypus,\
zebrafish, fugu, stickleback, medaka</TD></TR>\
<TR ALIGN=left><TD>RefSeq Genes</TD><TD>cow, frog</TD></TR>\
<TR ALIGN=left><TD>mRNAs</TD><TD>orangutan, elephant, rabbit, cat, horse,\
chicken, lizard, armadillo, tetraodon</TD></TR>\
<TR ALIGN=left><TD>None</TD><TD>marmoset, bushbaby, tree shrew, guinea pig,\
shrew, hedgehog, tenrec</TD></TR>\
</TABLE>\
<B>Table 2.</B> <EM>Gene tracks used for codon translation.</EM>\
</BLOCKQUOTE></P>\
\
<H2>Methods</H2>\
<P> \
Pairwise alignments with the mouse genome were generated for \
each species using blastz from repeat-masked genomic sequence. \
Pairwise alignments were then linked into chains using a dynamic programming\
algorithm that finds maximally scoring chains of gapless subsections\
of the alignments organized in a kd-tree.\
The scoring matrix and parameters for pairwise alignment and chaining\
were tuned for each species based on phylogenetic distance from the reference.\
High-scoring chains were then placed along the genome, with\
gaps filled by lower-scoring chains, to produce an alignment net.\
For more information about the chaining and netting process and \
parameters for each species, see the description pages for the Chain and Net \
tracks.</P>\
<P>\
An additional filtering step was introduced in the generation of the 30-way\
conservation track to reduce the number of paralogs and pseudogenes from the \
high-quality assemblies and the suspect alignments from the low-quality \
assemblies:\
the pairwise alignments of high-quality mammalian \
sequences (placental and marsupial) were filtered based on synteny; \
those for 2X mammalian genomes were filtered to retain only \
alignments of best quality in both the target and query (&quot;reciprocal \
best&quot;).</P>\
<P>\
The resulting best-in-genome pairwise alignments\
were progressively aligned using multiz/autoMZ, \
following the tree topology diagrammed above, to produce multiple alignments.\
The multiple alignments were post-processed to\
add annotations indicating alignment gaps, genomic breaks,\
and base quality of the component sequences.\
The annotated multiple alignments, in MAF format, are available for\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/multiz30way"\
TARGET=_blank>bulk download</A>.\
An alignment summary table containing an entry for each\
alignment block in each species was generated to improve\
track display performance at large scales.\
Framing tables were constructed to enable\
visualization of codons in the multiple alignment display.</P>\
<P>\
Conservation scoring was performed using the PhastCons package (A. Siepel),\
which computes conservation based on a two-state phylogenetic hidden Markov\
model (HMM).\
PhastCons measurements rely on a tree model containing the tree topology,\
branch lengths representing evolutionary distance at neutrally\
evolving sites, the background distribution of nucleotides, and a substitution\
rate matrix.  The \
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/phastCons30way/vertebrate.mod"\
TARGET=_blank>vertebrate tree model</A> for this track was\
generated using the phyloFit program from the phastCons package  \
(REV model, EM algorithm, medium precision) using multiple alignments of \
4-fold degenerate sites extracted from the 30way alignment\
(msa_view).  The 4d sites were derived from the \
<A HREF="https://genome.crg.es/gencode/" TARGET=_blank>Oct 2005 Gencode \
Reference Gene set</A>,\
which was filtered to select single-coverage long transcripts.  A second, \
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/phastCons30way/placental.mod" \
TARGET=_blank>mammalian tree model</A> including only placental mammals was used\
to generate\
the placental mammal conservation scoring. The phastCons parameters were\
tuned to produce 5% conserved elements in the genome for the vertebrate\
conservation measurement.  This parameter set (expected-length=45, \
target-coverage=.3, rho=.31) was then used to generate the placental\
mammal conservation scoring.</P>\
<P>\
The phastCons program computes conservation scores based on a phylo-HMM, a\
type of probabilistic model that describes both the process of DNA\
substitution at each site in a genome and the way this process changes from\
one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and\
Haussler 2005).  PhastCons uses a two-state phylo-HMM, with a state for\
conserved regions and a state for non-conserved regions.  The value plotted\
at each site is the posterior probability that the corresponding alignment\
column was "generated" by the conserved state of the phylo-HMM.  These\
scores reflect the phylogeny (including branch lengths) of the species in\
question, a continuous-time Markov model of the nucleotide substitution\
process, and a tendency for conservation levels to be autocorrelated along\
the genome (i.e., to be similar at adjacent sites).  The general reversible\
(REV) substitution model was used.  Unlike many conservation-scoring programs, \
note that phastCons does not rely on a sliding window\
of fixed size; therefore, short highly-conserved regions and long moderately\
conserved regions can both obtain high scores.  More information about\
phastCons can be found in Siepel et al. 2005.</P> \
<P> \
PhastCons currently treats alignment gaps as missing data, which\
sometimes has the effect of producing undesirably high conservation scores\
in gappy regions of the alignment.  We are looking at several possible ways\
of improving the handling of alignment gaps.</P>\
\
<H2>Credits</H2>\
<P> This track was created using the following programs:\
<UL>\
<LI> Alignment tools: blastz and multiz by Minmei Hou, Scott Schwartz and Webb \
Miller of the <A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Penn State Bioinformatics Group</A>\
<LI> Chaining and Netting:  axtChain, chainNet by Jim Kent at UCSC\
<LI> Conservation scoring: PhastCons, phyloFit, tree_doctor, msa_view by \
<A HREF="http://siepellab.labsites.cshl.edu/"\
TARGET=_blank>Adam Siepel</A> while at UCSC, now at Cold Spring Harbor Laboratory\
<LI> MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows\
by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC\
<LI> Tree image generator: phyloPng by Galt Barber, UCSC\
<LI> Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle \
display), and Brian Raney (gap annotation and codon framing) at UCSC\
</UL>\
</P>\
<P>The phylogenetic tree is based on Murphy et al. (2001) and general \
consensus in the vertebrate phylogeny community as of March 2007.\
</P>\
\
<H2>References</H2>\
\
<H3>Phylo-HMMs and phastCons:</H3>\
<p>\
Felsenstein J, Churchill GA.\
<a href="https://academic.oup.com/mbe/article/13/1/93/1055515"\
target="_blank">A Hidden Markov Model approach to\
variation among sites in rate of evolution</a>.\
<em>Mol Biol Evol</em>. 1996 Jan;13(1):93-104.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8583911" target="_blank">8583911</a>\
</p>\
\
<p>\
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K,\
Clawson H, Spieth J, Hillier LW, Richards S, <em>et al.</em>\
<a href="https://genome.cshlp.org/content/15/8/1034"\
target="_blank">Evolutionarily conserved elements in vertebrate, insect, worm,\
and yeast genomes</a>.\
<em>Genome Res</em>. 2005 Aug;15(8):1034-50.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16024819" target="_blank">16024819</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182216/" target="_blank">PMC1182216</a>\
</p>\
\
<p>\
Siepel A, Haussler D.\
<a href="http://compgen.cshl.edu/~acs/phylohmm.pdf"\
target="_blank">Phylogenetic Hidden Markov Models</a>.\
In: Nielsen R, editor. Statistical Methods in Molecular Evolution.\
New York: Springer; 2005. pp. 325-351.\
</p>\
\
<p>\
Yang Z.\
<a href="https://www.genetics.org/content/139/2/993"\
target="_blank">A space-time process model for the evolution of DNA\
sequences</a>.\
<em>Genetics</em>. 1995 Feb;139(2):993-1005.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/7713447" target="_blank">7713447</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1206396/" target="_blank">PMC1206396</a>\
</p>\
\
<H3>Chain/Net:</H3>\
<p>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<a href="https://www.pnas.org/content/100/20/11484"\
target="_blank">Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<H3>Multiz:</H3>\
<p>\
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM,\
Baertsch R, Rosenbloom K, Clawson H, Green ED, <em>et al.</em>\
<a href="https://genome.cshlp.org/content/14/4/708.abstract"\
target="_blank">Aligning multiple genomic sequences with the threaded blockset aligner</a>.\
<em>Genome Res</em>. 2004 Apr;14(4):708-15.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15060014" target="_blank">15060014</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC383317/" target="_blank">PMC383317</a>\
</p>\
\
<H3>Blastz:</H3>\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<a href="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
target="_blank">Scoring pairwise genomic sequence alignments</a>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<p>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<a href="https://genome.cshlp.org/content/13/1/103.abstract"\
target="_blank">Human-mouse alignments with BLASTZ</a>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
\
<H3>Phylogenetic Tree:</H3>\
<p>\
Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E,\
Ryder OA, Stanhope MJ, de Jong WW, Springer MS.\
<a href="https://science.sciencemag.org/content/294/5550/2348"\
target="_blank">Resolution of the early placental mammal radiation using Bayesian phylogenetics</a>.\
<em>Science</em>. 2001 Dec 14;294(5550):2348-51.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11743200" target="_blank">11743200</a>\
</p>\
	compGeno	1	altColor 0,90,10\
color 0, 10, 100\
frames multiz30wayFrames\
group compGeno\
irows on\
itemFirstCharCase noChange\
longLabel Multiz Alignments of 30 Vertebrates\
noInherit on\
pairwiseHeight 12\
parent cons30wayViewalign on\
priority 100\
sGroup_Glires rn4 cavPor2 oryCun1\
sGroup_Placental_Mammal tupBel1 sorAra1 eriEur1 canFam2 felCat3 equCab1 bosTau3 dasNov1 loxAfr1 echTel1\
sGroup_Primates hg18 panTro2 rheMac2 ponAbe2 calJac1 otoGar1\
sGroup_Vertebrate monDom4 ornAna1 galGal3 anoCar1 xenTro2 gasAcu1 danRer5 tetNig1 fr2 oryLat1\
shortLabel Multiz Align\
speciesCodonDefault mm9\
speciesDefaultOff rheMac2 calJac1 panTro2 cavPor2 tupBel1 otoGar1 dasNov1 oryCun1 felCat3 loxAfr1 bosTau3 eriEur1 sorAra1 echTel1 ornAna1 anoCar1 xenTro2 danRer5 tetNig1 fr2 oryLat1\
speciesGroups Glires Primates Placental_Mammal Vertebrate\
subGroups view=align clade=vert\
summary multiz30waySummary\
track multiz30way\
treeImage phylo/mm9_30way.gif\
type wigMaf 0.0 1.0\

nscanGene	N-SCAN	genePred nscanPep	N-SCAN Gene Predictions	0	100	34	139	34	144	197	144	0	0	0			<H2>Description</H2>\
<P>\
This track shows gene predictions using the N-SCAN gene structure prediction\
software provided by the Computational Genomics Lab at Washington University \
in St. Louis, MO, USA.\
</P>\
\
<H2>Methods</H2>\
<P>\
N-SCAN combines biological-signal modeling in the target genome sequence along\
with information from a multiple-genome alignment to generate de novo gene\
predictions. It extends the TWINSCAN target-informant genome pair to allow for\
an arbitrary number of informant sequences as well as richer models of\
sequence evolution. N-SCAN models the phylogenetic relationships between the\
aligned genome sequences, context-dependent substitution rates, insertions,\
and deletions.\
</P>\
<P>Mouse N-SCAN uses human (hg18) as the informant and iterative pseudogene masking.</P>\
\
<H2>Credits</H2>\
<P>\
Thanks to <A HREF="https://mblab.wustl.edu/" \
TARGET=_blank>Michael Brent's Computational Genomics Group</A> at Washington \
University St. Louis for providing this data.\
</P>\
<p>\
Special thanks for this implementation of N-SCAN to Aaron Tenney in\
the Brent lab, and Robert Zimmermann, currently at Max F. Perutz\
Laboratories in Vienna, Austria.\
</p>\
\
<H2>References</H2>\
<p>\
Gross SS, Brent MR.\
<a href="https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.379" target="_blank">\
Using multiple alignments to improve gene prediction</a>.\
<em>J Comput Biol</em>. 2006 Mar;13(2):379-93.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16597247" target="_blank">16597247</a>\
</p>\
\
<P>\
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM,\
Rusch DB, Town CD <EM>et al</EM>.\
<a href="https://academic.oup.com/nar/article/31/19/5654/1092988/Improving-the-Arabidopsis-genome-annotation-using"\
target="_blank">Improving the <EM>Arabidopsis</EM> genome annotation using maximal transcript \
alignment assemblies</A>.\
<em>Nucleic Acids Res</em>. 2003 Oct 1;31(19):5654-66.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500829" target="_blank">14500829</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC206470/" target="_blank">PMC206470</a>\
</p>\
\
<P>\
Korf I, Flicek P, Duan D, Brent MR.\
<A HREF="https://academic.oup.com/bioinformatics/article/17/suppl_1/S140/261903/Integrating-genomic-homology-into-gene-structure"\
TARGET=_blank>Integrating genomic homology into gene structure prediction</A>.\
<em>Bioinformatics</em>. 2001;17 Suppl 1:S140-8.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11473003" target="_blank">11473003</a>\
</p>\
\
<P>\
van Baren MJ, Brent MR.\
<A HREF="https://genome.cshlp.org/content/16/5/678.abstract"\
TARGET=_blank>Iterative gene prediction and pseudogene removal improves\
genome annotation</A>.\
<em>Genome Res</em>. 2006 May;16(5):678-85.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16651666" target="_blank">16651666</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1457044/" target="_blank">PMC1457044</a>\
</p>\
	genes	1	baseColorDefault genomicCodons\
baseColorUseCds given\
color 34,139,34\
group genes\
informant Mouse N-SCAN uses human (hg18) as the informant and iterative pseudogene masking.\
longLabel N-SCAN Gene Predictions\
shortLabel N-SCAN\
track nscanGene\
type genePred nscanPep\
visibility hide\

wgEncodeNhgriBip	NHGRI BiP	bed 8 +	ENCODE NHGRI Elnitski Bidirectional Promoters	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
\
<p>Bidirectional promoters are the regulatory regions that fall between\
pairs of genes, where the 5' ends of the genes within a pair are positioned\
in close proximity to one another. This spacing facilitates the initiation\
of transcription of both genes, creating two transcription forks that advance\
in opposite directions. The formal definition of a bidirectional promoter\
requires that the transcription initiation sites are separated by no more than\
1,000 bp from one another. Using these criteria we have comprehensively\
annotated the human and mouse genomes for the presence of bidirectional\
promoters, using in silico approaches. The identification of these promoters\
is contingent upon the presence of adjacent, oppositely oriented pairs of\
genes, because few distinguishing features are available to uniquely identify\
bidirectional promoters de novo. Genomic annotations used for our\
identification phase include:\
<ul>\
<li><em>A</em>) <a href="hgTrackUi?g=knownGene">UCSC known genes</a>\
annotations (items with score=800).\
<li><em>B</em>) <a href="hgTrackUi?g=mrna">GenBank mRNA</a> annotations\
(score=600).\
<li><em>C</em>) <a href="hgTrackUi?g=intronEst">spliced ESTs</a> (score=400).\
</ul>\
The annotations for protein coding genes (<em>A</em>) are strongly supported\
and therefore provide a high quality dataset for mapping bidirectional\
promoters. In contrast, bidirectional promoters supported by spliced ESTs\
(<em>C</em>) alone have varying levels of evidence, ranging from one\
characterized transcript to hundreds of them. For this reason, the mRNA\
annotation (<em>B</em>) from GenBank provides a stringent level of validation\
for the start sites of the EST transcripts. As a large class of regulatory\
sequences, bidirectional promoters exemplify a rich source of unexplored\
biological information in the human genome. When compared to the mouse genome,\
these promoters are identifiable as truly orthologous locations, being\
maintained in regions of conserved synteny (including both genes and the\
intervening promoter region) that have undergone no rearrangements since the\
last common ancestor of mammals, and in some cases fish. We use this approach\
to annotate orthologous bidirectional promoters in nonhuman species until\
genomic annotations become available.\
</p>\
\
<h2>Methods</h2>\
\
<h3>Assigning Orthologous Regions</h3>\
<p>A multi-stage approach to mapping orthology at bidirectional promoters was\
developed. Orthology assignments are strongest in coding regions. Therefore we\
began by mapping single human genes regulated by bidirectional promoters from\
the Known Genes annotations onto the mouse genome. Orthology assignments were\
determined using the "chains and nets" data from the UCSC Human Genome Browser\
mysql tables. Chains in the Genome Browser represent sequences of gapless\
aligned blocks. Nets provide a hierarchical ordering of those chains. Level 1\
chains contain the longest, best-scoring sequence chains that span any\
selected region. Subsequent levels in the net represent the results of\
rearrangements, duplications, insertions and deletions that may have disrupted\
the presence of conserved synteny derived from an ancestral sequence.\
</p>\
\
<h3>Confirming Orthologous Genes</h3>\
<p>After determining the orthology assignments using the UCSC chains and nets\
data, we used the Known Gene annotations or spliced ESTs to search the identity\
of genes within the corresponding region. Known Genes represent protein-coding\
genes and therefore can be verified by chains and nets alignments, followed by\
confirmation of protein identity in both species. Spliced ESTs carry less\
descriptive information than protein coding genes and therefore were validated\
in the second species by their presence in an orthologous region, showing\
conserved synteny of the two genes within a pair, and meeting the criteria of\
less than 1,000 bp of intergenic distance between those transcripts. Our method\
for mapping bidirectional promoters in spliced EST datasets is described in\
more detail in a previous publication. If the program verified evidence for\
orthology and conserved-syntenic gene arrangement, then the orthologous\
bidirectional promoter was confirmed. After orthologous assignments were\
confirmed for pairs of human genes, the reciprocal assignments were analyzed\
from mouse to human.\
\
Currently orthologous bidirectional promoter regions (that have been identified\
using UCSC known genes) have been mapped in human, chimp, macaque, mouse, rat,\
dog and cow genomes).\
</p>\
\
<h2>Credits</h2>\
\
<p>These data were produced by Mary Q. Yang in the\
<a href="https://www.genome.gov/12514761" title="https://www.genome.gov/12514761"\
 TARGET=_BLANK>Elnitski lab</a> at NHGRI, NIH. (contact:\
 <A HREF="mailto:&#101;&#108;&#110;&#105;&#116;&#115;ki&#64;&#109;&#97;&#105;l.n&#105;&#104;.g&#111;&#118;">\
 &#101;&#108;&#110;&#105;&#116;&#115;ki&#64;&#109;&#97;&#105;l.n&#105;&#104;.g&#111;&#118;</A>)\
 <!-- above address is elnitski at mail.nih.gov -->\
</p>\
\
<h2>References</h2>\
\
<p>\
Piontkivska H, Yang MQ, Larkin DM, Lewin HA, Reecy J, Elnitski L.\
<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-10-189" target="_blank">\
Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and\
identification of species-specific transcripts</a>.\
<em>BMC Genomics</em>. 2009 Apr 24;10:189.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19393065" target="_blank">19393065</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688522/" target="_blank">PMC2688522</a>\
</p>\
\
<p>\
Yang MQ, Elnitski LL.\
<a href="https://link.springer.com/chapter/10.1007%2F978-3-540-72031-7_33" target="_blank">\
A computational study of bidirectional promoters in the human genome\
</a>.\
<em>Springer Lecture Series: Notes in Bioinformatics</em> 2007.\
</p>\
\
<p>\
Yang MQ, Elnitski L.\
Orthology of Bidirectional Promoters Enables Use of a Multiple Class Predictor for Discriminating\
Functional Elements in the Human Genome.\
Proceedings of the 2007 International Conference on Bioinformatics &amp; Computational Biology.\
<!-- Re-add link when WORLDCOMP archives are updated:\
http://www.world-academy-of-science.org/past_events/ws/conferences/2007\
\
<a href="http://www.world-academy-of-science.org/worldcomp07/ws/BIOCOMP07" target="_blank">\
Proceedings of the 2007 International Conference on Bioinformatics &amp; Computational Biology\
</a>.\
-->\
pp. 218-228. 2007. ISBN: 1-60132-042-6.\
</p>\
\
<p>\
Yang MQ, Koehly LM, Elnitski LL.\
<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030072" target="_blank">\
Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and\
ovarian cancer genes</a>.\
<em>PLoS Comput Biol</em>. 2007 Apr 20;3(4):e72.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17447839" target="_blank">17447839</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1853124/" target="_blank">PMC1853124</a>\
</p>\
\
<p>\
Yang MQ, Taylor J, Elnitski L.\
<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-S6-S9"\
target="_blank">Comparative analyses of bidirectional promoters in vertebrates</a>.\
<em>BMC Bioinformatics</em>. 2008 May 28;9 Suppl 6:S9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18541062" target="_blank">18541062</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2423431/" target="_blank">PMC2423431</a>\
</p>\
\
<H2>Data Release Policy</H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the table<EM>metadata</EM> as <EM>dateUnrestricted</EM> and on the\
download page.  The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
	regulation	1	compareGenomeLinks hg18=Human_(March_2006) panTro2=Chimpanzee_(March_2006) rheMac2=Rhesus_(January_2006) rn4=Rat_(November_2004) canFam2=Dog_(May_05) bosTau4=Cow_(October_2007)\
dataVersion ENCODE Feb 2009 Freeze\
dateSubmitted 2009-01-27\
dateUnrestricted 2009-10-27\
group regulation\
longLabel ENCODE NHGRI Elnitski Bidirectional Promoters\
noScoreFilter on\
priority 0\
shortLabel NHGRI BiP\
track wgEncodeNhgriBip\
type bed 8 +\
visibility hide\

NIAGene	NIA Gene Index	psl .	NIA Mouse Gene Index	0	100	0	60	120	200	220	255	1	0	0		http://lgsun.grc.nia.nih.gov/geneindex/mm9/bin/giT.cgi?genename=$$	<H2>Description</H2>\
<P>\
This track displays alignments of the National Institute on Aging (NIA)\
Mouse Gene Index (mm9) to the mouse genome.\
<H2>Methods</H2>\
<P>\
The index was assembled from Blat alignments of the mouse\
genome (mm9/July 2007).\
<P>\
See the <A HREF="https://lgsun.grc.nia.nih.gov/" \
TARGET=_blank>NIA Mouse cDNA Project home page</A> for more information.</P>\
\
<H2>Credits</H2>\
<P>\
This track was produced by Alexei A. Sharov, Dawood B. Dudekula and Minoru\
S. H. Ko at the <A HREF="https://www.nia.nih.gov/" TARGET=_blank>NIA</A>, \
National Institutes of Health.  The research was supported by the NIA \
Intramural Research Program.</P>\
\
<H2>References</H2>\
<p>\
Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey\
UC <em>et al</em>.\
<a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0000074"\
target="_blank">Transcriptome analysis of mouse stem cells and early embryos</a>.\
<em>PLoS Biol</em>. 2003 Dec;1(3):E74.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14691545" target="_blank">14691545</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC300684/" target="_blank">PMC300684</a>\
</p>\
\
<p>\
Sharov AA, Dudekula DB, Ko MS.\
<a href="https://genome.cshlp.org/content/15/5/748.full" target="_blank">\
Genome-wide assembly and analysis of alternative transcripts in mouse</a>.\
<em>Genome Res</em>. 2005 May;15(5):748-54.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15867436" target="_blank">15867436</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088304/" target="_blank">PMC1088304</a>\
</p>\
	genes	1	altColor 200,220,255\
color 0,60,120\
group genes\
longLabel NIA Mouse Gene Index\
shortLabel NIA Gene Index\
spectrum on\
track NIAGene\
type psl .\
url http://lgsun.grc.nia.nih.gov/geneindex/mm9/bin/giT.cgi?genename=$$\
visibility hide\

laminB1Super	NKI Nuc Lamina		NKI Nuclear Lamina Associated Domains (LaminB1 DamID)	0	100	0	0	0	127	127	127	0	0	0			<H2>Overview</H2>\
\
<div class="figure" style="float: right;  width: 439px; border: thin silver solid ; margin: 0 20px\
20px 20px; padding: 20px 10px 10px 10px; text-align: center; font-size: 0.9em; background-color:\
#e9e9e9;"> <img src="../images/laminB1Mm9.png" alt="Nuclear Lamina and Chromosomal Organization in\
Mouse Cells"> <p>Model of chromosome organization in interphase, summarizing the main results\
presented in this paper. Large, discrete chromosomal domains are dynamically associated with the\
nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al.\
2010).</p> </div>\
\
<P>The three-dimensional organization of chromosomes within the nucleus and its dynamics during\
differentiation are largely unknown. To visualize this process in molecular detail, high-resolution\
maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem\
cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into\
terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse\
embryonic fibroblasts were profiled.</P>\
\
<P>This revealed that a basal chromosome architecture present in embryonic stem cells is\
cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal\
differentiation. This remodeling involves both individual transcription units and multi-gene\
regions, and affects many genes that determine cellular identity. Often, genes that move away from\
the lamina are concomitantly activated; many others however remain inactive yet become unlocked for\
activation in a next differentiation step. These results suggest that lamina-genome interactions are\
widely involved in the control of gene expression programs during lineage commitment and terminal\
differentiation.</P>\
\
<h3> NKI mouse LaminB1 ESC track </h3> <P> The mouse LaminB1 ESC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
stem cells. </P>\
\
<h3> NKI mouse LaminB1 NPC track </h3> <P> The mouse LaminB1 NPC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural\
progenitor cells. </P>\
\
<h3> NKI mouse LaminB1 AC track </h3> <P> The mouse LaminB1 AC track shows a high resolution map of\
the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes.\
</P>\
\
<h3> NKI mouse LaminB1 MEF track </h3> <P> The mouse LaminB1 MEF track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
fibroblasts. </P>\
\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for\
the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5  standard deviations.\
</P>\
\
<P> For an example region see genomic location: <a\
href="/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=chr14:92,000,000-96,000,000&refGene=\
pack&laminB1Super=show&laminB1_ES=full&laminB1_AC=full&laminB1_NP=full&laminB1_EF=full">chr14:92,000\
,000-96,000,000</a> (Fig 3A, Peric-Hupkes, Meuleman <EM>et al.</EM>, 2010). </P>\
\
\
<H2>Methods</H2>\
\
<P>The DamID technique was applied to generate high-resolution maps of NL interactions for the\
entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact\
in vivo with a protein of interest. </P>\
\
\
\
\
<P>DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein\
consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was\
introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most\
eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by\
immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique\
methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. <a\
href="https://chromatingenomics.org/damid/">Unfused Dam</a> was used as a reference. The\
data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only.</P>\
\
<P> Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on\
a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize\
unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed\
by quantile normalization across the single channel data of all hybridizations. Replicate arrays\
were averaged. </P>\
\
\
<H2>Verification</H2>\
\
<P> The data are based on two independent biological replicates for each cell type, performed on\
separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1\
associated regions are preferentially located at the nuclear periphery. The array platform, the <A\
HREF="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">raw and normalized\
data</A> have been deposited at the <a href="https://www.ncbi.nlm.nih.gov/geo/">NCBI Gene Expression\
Omnibus (GEO)</a> under accession number <a\
href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">GSE17051</A>. </P>\
\
\
<H2>Credits</H2>\
\
<P> The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van\
Steensel at the <A HREF="https://chromatingenomics.org/" TARGET=_blank>Van Steensel Lab</A>,\
Netherlands Cancer Institute. </P>\
\
\
<H2>References</H2>\
<p>\
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P,\
Kerkhoven RM, van Lohuizen M <em>et al</em>.\
<a href="https://www.sciencedirect.com/science/article/pii/S1097276510003217" target="_blank">\
Molecular maps of the reorganization of genome-nuclear lamina interactions during\
differentiation</a>.\
<em>Mol Cell</em>. 2010 May 28;38(4):603-13.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20513434" target="_blank">20513434</a>\
</p>\
	regulation	0	group regulation\
html laminB1Mm9\
longLabel NKI Nuclear Lamina Associated Domains (LaminB1 DamID)\
shortLabel NKI Nuc Lamina\
superTrack on\
track laminB1Super\

numtSeq	NumtS Sequence	bed 3 .	Mouse NumtS mitochondrial sequence	0	100	0	0	0	127	127	127	0	0	0			<h2>Description and display conventions</h2>\
\
<p> <b>NumtS</b> (Nuclear mitochondrial sequences) are mitochondrial fragments inserted in nuclear\
genomic sequences. The most credited hypothesis concerning their generation suggests that in presence\
of mutagenic agents, or under stress conditions, fragments of mtDNA escape from mitochondria, reach\
the nucleus and insert into chromosomes during break repair; although NumtS can also derive from\
duplication of genomic fragments. NumtS may be a cause of contamination during human mtDNA sequencing\
and hence frequent false low heteroplasmic evidences have been reported. The Bioinformatics group\
chaired by M. Attimonelli (University of Bari, Italy) has produced the RMmsNumtS (Reference Mus musculus\
NumtS) compilation annotating 148 Mouse assembled NumtS. To allow the scientific community to access \
the compilation and to perform genomics comparative analyses inclusive of the NumtS data, the\
group has designed the Mouse NumtS tracks described below. </p>\
\
<p>The NumtS tracks show nuclear and mitochondrial regions, based on the High Score Pairs (HSPs)\
obtained by aligning the mitochondrial reference genome (NC_005089) with the mm9 assembly of the\
mouse genome.</p> \
\
<ol> \
\	<li><b>"NumtS (Nuclear mitochondrial Sequences)" Track</b> \
\	<p> The "NumtS\
mitochondrial sequences" track shows the mapping of the HSPs returned by BlastN on the nuclear\
genome. The shading of the items reflect the similarity returned by BlastN, and the direction of\
the arrows is concordant with the strand of the alignment. For every item, a link pointing to the\
mitochondrial mapping is provided, thus allowing a fast cross among the NumtS genomic contexts. </p>\
\	</li>\
\
\	<li><b>"NumtS assembled" Track</b> \
\	<p> The "NumtS assembled" track shows items obtained by\
assembling HSPs annotated in the "NumtS" track fulfilling the following conditions:</p>\
\
\	\	<ul>\
\	\	\	<li>The orientation of their alignments must be concordant.</li> \
\	\	\	<li>The distance between them must be less than 2 kb, on the mitochondrial genome as \
\	\	\	well as on the nuclear genome.</li> \
\	\	</ul> \
\	\	\
\	<p>Exceptions for the second condition arise when a long repetitive element is present between\
\	 two HSPs.</p></li>\
\
\	<li><b>"NumtS on mitochondrion" Track</b>\
\	<p>The "NumtS on mitochondrion" track shows the mapping\
of the HSPs on the mitochondrial genome. The shading of the items reflects the similarity returned\
by BlastN, and the direction of the arrows is concordant with the strand of the alignment. For every\
item, a link pointing to the nuclear mapping is provided.</p></li>\
\
\	<li><b>"Mouse NumtS on mitochondrion SNP" Track</b> \
\	<p>The "Mouse NumtS SNP" shows the mapping of\
the HSPs on the mitochondrial genome, with the SNPs which fall within, derived from comparison\
with the mm9 assembly. No shading is here provided. For every item, a link pointing to the nuclear\
mapping is provided.</p></li>\
</ol>\
\
<h2>Methods</h2> \
\
<p>NumtS mappings were obtained by running Blast2seq (program: BlastN) between\
each chromosome of the Mouse Genome (mm9 assembly) and the mouse mitochondrial reference sequence (AC:\
NC_005089), fixing the e-value threshold to 1e-03. The assembling of the HSPs was performed with\
spreadsheet interpolation and manual inspection. BED format is used for the first three annotation\
tracks, while for the last one the SAM/BAM format is preferred.</p>\
\
<h2>Credits</h2>\
\
<p>These data were provided by Francesco Maria Calabrese, Domenico Simone and\
Marcella Attimonelli from the Department of Biochemistry and Molecular Biology "Ernesto \
Quagliariello" (University of Bari, Italy). Manual inspection and format details are carried out \
by Francesco Maria Calabrese, Domenico Simone and Luana Raddi.</p>\
\
<h2>References</h2>\
\
<p>\
Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M.\
<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-9-267" target="_blank">\
The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human\
NumtS</a>.\
<em>BMC Genomics</em>. 2008 Jun 3;9:267.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18522722" target="_blank">18522722</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447851" target="_blank">PMC2447851</a>\
</p>\
\
<p>\
Simone D, Calabrese FM, Lang M, Gasparre G, Attimonelli M.\
<a href="https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-517" target="_blank">\
The reference human nuclear mitochondrial sequences compilation validated and implemented on the\
UCSC genome browser</a>.\
<em>BMC Genomics</em>. 2011 Oct 20;12:517.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22013967" target="_blank">22013967</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228558" target="_blank">PMC3228558</a>\
</p>\
\
\
	varRep	1	compositeTrack on\
group varRep\
html numtSeqMm9\
longLabel Mouse NumtS mitochondrial sequence\
noInherit on\
shortLabel NumtS Sequence\
track numtSeq\
type bed 3 .\
visibility hide\

knownGeneOld4	Old UCSC Genes	genePred	Previous Version of UCSC Genes	0	100	82	82	160	168	168	207	0	0	0			<H2>Description</H2>\
<P>\
The Old UCSC Genes track shows genes from the previous version of\
the UCSC Genes build.  This is similar to the current version is\
based on less Genbank, RefSeq, and UniProt data.\
</P>\
<P>\
Read the <A HREF="../cgi-bin/hgTrackUi?c=chrX&g=knownGene">description</A> \
of how the current version of the UCSC Genes track was built.\
</P>\
	genes	1	baseColorDefault genomicCodons\
baseColorUseCds given\
color 82,82,160\
group genes\
hgsid on\
longLabel Previous Version of UCSC Genes\
oldToNew kg4ToKg5\
shortLabel Old UCSC Genes\
track knownGeneOld4\
type genePred\
visibility hide\

oreganno	ORegAnno	bed 4 +	Regulatory elements from ORegAnno	0	100	102	102	0	178	178	127	0	0	0			<H2>Description</H2>\
<P>\
This track displays literature-curated regulatory regions, transcription\
factor binding sites, and regulatory polymorphisms from\
<a href="http://www.oreganno.org/"\
target="_blank">ORegAnno</a> (Open Regulatory Annotation). For more detailed\
information on a particular regulatory element, follow the link to ORegAnno\
from the details page. \
<!--\
<b><font color="666600">O</font><font color="CC0033">Reg</font><font color="BBBB55">Anno</font></b> (Open Regulatory Annotation).\
-->\
</P>\
\
<H2>Display Conventions and Configuration</H2>\
\
<p>The display may be filtered to show only selected region types, such as:</p>\
\
<ul style="background-color: #fff; padding: 10px 15px 10px 30px; display: inline; display: inline-block; -webkit-border-radius: 3px;\
-moz-border-radius: 3px; border-radius: 3px; border: 1px solid #c4c4c4;">\
<li style="color: #56B4E9;">regulatory regions (shown in light blue)</li>\
<li style="color: #0072B2;">regulatory polymorphisms (shown in dark blue)</li>\
<li style="color: #E69F00;">transcription factor binding sites (shown in orange)</li>\
<li style="color: #D55E00;">regulatory haplotypes (shown in red)</li>\
<li style="color: #009E73;">miRNA binding sites (shown in blue-green)</li>\
</ul>\
\
<p>To exclude a region type, uncheck the appropriate box in the list at the top of \
the Track Settings page. </p>\
\
<H2>Methods</H2>\
<P>\
An ORegAnno record describes an experimentally proven and published regulatory\
region (promoter, enhancer, etc.), transcription factor binding site, or\
regulatory polymorphism.  Each annotation must have the following attributes:\
<ul>\
<li>A stable ORegAnno identifier.\
<li>A valid taxonomy ID from the NCBI taxonomy database.\
<li>A valid PubMed reference.  \
<li>A target gene that is either user-defined, in Entrez Gene or in EnsEMBL.\
<li>A sequence with at least 40 flanking bases (preferably more) to allow the\
site to be mapped to any release of an associated genome.\
<li>At least one piece of specific experimental evidence, including the\
biological technique used to discover the regulatory sequence. (Currently\
only the evidence subtypes are supplied with the UCSC track.)\
<li>A positive, neutral or negative outcome based on the experimental results\
from the primary reference. (Only records with a positive outcome are currently\
included in the UCSC track.)\
</ul>\
The following attributes are optionally included:\
<ul>\
<li>A transcription factor that is either user-defined, in Entrez Gene\
or in EnsEMBL.\
<li>A specific cell type for each piece of experimental evidence, using the\
eVOC cell type ontology.\
<li>A specific dataset identifier (e.g. the REDfly dataset) that allows\
external curators to manage particular annotation sets using ORegAnno's\
curation tools.\
<li>A &quot;search space&quot; sequence that specifies the region that was\
assayed, not just the regulatory sequence.  \
<li>A dbSNP identifier and type of variant (germline, somatic or artificial)\
for regulatory polymorphisms.\
</ul>\
Mapping to genome coordinates is performed periodically to current genome\
builds by BLAST sequence alignment.  \
The information provided in this track represents an abbreviated summary of the \
details for each ORegAnno record. Please visit the official ORegAnno entry\
(by clicking on the ORegAnno link on the details page of a specific regulatory\
element) for complete details such as evidence descriptions, comments,\
validation score history, etc.\
</P>\
\
<H2>Credits</H2>\
<P>\
ORegAnno core team and principal contacts: Stephen Montgomery, Obi Griffith, \
and Steven Jones from <A HREF="https://www.bcgsc.ca/"\
TARGET=_blank>Canada's Michael Smith Genome Sciences Centre</A>, Vancouver, \
British Columbia, Canada.</P>\
<P>\
The ORegAnno community (please see individual citations for various\
features): <A HREF="http://www.oreganno.org/"\
TARGET="_blank">ORegAnno Citation</A>.\
\
<H2>References</H2>\
<p>\
Lesurf R, Cotto KC, Wang G, Griffith M, Kasaian K, Jones SJ, Montgomery SB, Griffith OL, Open\
Regulatory Annotation Consortium..\
<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1203" target="_blank">\
ORegAnno 3.0: a community-driven resource for curated regulatory annotation</a>.\
<em>Nucleic Acids Res</em>. 2016 Jan 4;44(D1):D126-32.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26578589" target="_blank">26578589</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702855/" target="_blank">PMC4702855</a>\
</p>\
\
<p>\
Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M,\
Haeussler M <em>et al</em>.\
<a href="https://academic.oup.com/nar/article/36/suppl_1/D107/2508119/ORegAnno-an-open-access-\
community-driven-resource" target="_blank">\
ORegAnno: an open-access community-driven resource for regulatory annotation</a>.\
<em>Nucleic Acids Res</em>. 2008 Jan;36(Database issue):D107-13.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18006570" target="_blank">18006570</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2239002/" target="_blank">PMC2239002</a>\
</p>\
\
<P>\
Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, \
Prychyna Y, Zhang X, Jones SJ. \
<A HREF="https://academic.oup.com/bioinformatics/article/22/5/637/206022/ORegAnno-an-open-access-\
database-and-curation" TARGET="_blank">ORegAnno: an open access database and curation system for \
literature-derived promoters, transcription factor binding sites and regulatory variation</A>.\
<em>Bioinformatics</em>. 2006 Mar 1;22(5):637-40.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/16397004" target="_blank">16397004</a>\
</p>\
\
	regulation	1	color 102,102,0\
group regulation\
longLabel Regulatory elements from ORegAnno\
shortLabel ORegAnno\
track oreganno\
type bed 4 +\
visibility hide\

orfeomeMrna	ORFeome Clones	psl	ORFeome Collaboration Gene Clones	0	100	34	139	34	144	197	144	0	0	0			<h2>Description</h2>\
\
<p>\
This track shows alignments of mouse clones from the\
<a href="http://www.orfeomecollaboration.org/" target="_blank">\
ORFeome Collaboration</a>.  The goal of the project is to be an\
&quot;unrestricted source of fully sequence-validated full-ORF human cDNA\
clones in a format allowing easy transfer of the ORF sequences into\
virtually any type of expression vector.  A major goal is to provide\
at least one fully-sequenced full-ORF clone for each human gene.&quot;\
This track is updated automatically as new clones become available.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
The track follows the display conventions for\
<a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction\
tracks</a>.</p>\
\
<h2>Methods</h2>\
\
<p>\
ORFeome mouse clones were obtained from GenBank and aligned against the\
genome using the blat program. When a single clone aligned in multiple\
places, the alignment having the highest base identity was found.  Only alignments\
having a base identity level within 0.5% of the best and at least 96% base\
identity with the genomic sequence were kept.\
</p>\
\
<h2>Credits and References</h2>\
\
<p>\
Visit the ORFeome Collaboration\
<a href="http://www.orfeomecollaboration.org/?pageID=32" target="_blank">\
members page</a> for a list of credits and references.\
</p>\
	genes	1	baseColorDefault diffCodons\
baseColorUseCds genbank\
baseColorUseSequence genbank\
color 34,139,34\
group genes\
indelDoubleInsert on\
indelQueryInsert on\
longLabel ORFeome Collaboration Gene Clones\
shortLabel ORFeome Clones\
showCdsAllScales .\
showCdsMaxZoom 10000.0\
showDiffBasesAllScales .\
showDiffBasesMaxZoom 10000.0\
track orfeomeMrna\
type psl\
visibility hide\

xenoMrna	Other mRNAs	psl xeno	Non-Mouse mRNAs from GenBank	0	100	0	0	0	127	127	127	1	0	0			<h2>Description</h2>\
\
<p>\
This track displays translated blat alignments of vertebrate and\
invertebrate mRNA in\
<a href="https://www.ncbi.nlm.nih.gov/genbank/" target="_blank">\
GenBank</a> from organisms other than mouse.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track follows the display conventions for\
<a href="../goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank">\
PSL alignment tracks</a>. In dense display mode, the items that\
are more darkly shaded indicate matches of better quality.\
</p>\
\
<p>\
The strand information (+/-) for this track is in two parts.  The\
first + indicates the orientation of the query sequence whose\
translated protein produced the match (here always 5' to 3', hence +).\
The second + or - indicates the orientation of the matching\
translated genomic sequence. Because the two orientations of a DNA\
sequence give different predicted protein sequences, there are four\
combinations.  ++ is not the same as --, nor is +- the same as -+.\
</p>\
\
<p>\
The description page for this track has a filter that can be used to change\
the display mode, alter the color, and include/exclude a subset of items\
within the track. This may be helpful when many items are shown in the track\
display, especially when only some are relevant to the current task.\
</p>\
\
<p>\
To use the filter:\
<ol>\
<li>Type a term in one or more of the text boxes to filter the mRNA\
display. For example, to apply the filter to all mRNAs expressed in a specific\
organ, type the name of the organ in the tissue box. To view the list of\
valid terms for each text box, consult the table in the Table Browser that\
corresponds to the factor on which you wish to filter. For example, the\
&quot;tissue&quot; table contains all the types of tissues that can be\
entered into the tissue text box. Multiple terms may be entered at once,\
separated by a space. Wildcards may also be used in the filter.</li>\
<li>If filtering on more than one value, choose the desired combination\
logic. If &quot;and&quot; is selected, only mRNAs that match all filter\
criteria will be highlighted. If &quot;or&quot; is selected, mRNAs that\
match any one of the filter criteria will be highlighted.</li>\
<li>Choose the color or display characteristic that should be used to\
highlight or include/exclude the filtered items. If &quot;exclude&quot; is\
chosen, the browser will not display mRNAs that match the filter criteria.\
If &quot;include&quot; is selected, the browser will display only those\
mRNAs that match the filter criteria.</li>\
</ol>\
</p>\
\
<p>\
This track may also be configured to display codon coloring, a feature that\
allows the user to quickly compare mRNAs against the genomic sequence. For more\
information about this option, go to the\
<a href="../goldenPath/help/hgCodonColoringMrna.html" target="_blank">\
Codon and Base Coloring for Alignment Tracks</a> page.\
Several types of alignment gap may also be colored;\
for more information, go to the\
<a href="../goldenPath/help/hgIndelDisplay.html" target="_blank">\
Alignment Insertion/Deletion Display Options</a> page.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
The mRNAs were aligned against the mouse genome using translated blat.\
When a single mRNA aligned in multiple places, the alignment having the\
highest base identity was found.  Only those alignments having a base\
identity level within 1% of the best and at least 25% base identity with the\
genomic sequence were kept.\
</p>\
\
<H2>Credits</h2>\
\
<p>\
The mRNA track was produced at UCSC from mRNA sequence data\
submitted to the international public sequence databases by\
scientists worldwide.\
</p>\
\
<h2>References</h2>\
<p>\
Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.\
<a href="https://academic.oup.com/nar/article/41/D1/D36/1068219/GenBank" target="_blank">\
GenBank</a>.\
<em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D36-42.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23193287" target="_blank">23193287</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531190/" target="_blank">PMC3531190</a>\
</p>\
\
<P>\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
<A HREF="https://academic.oup.com/nar/article/32/suppl_1/D23/2505202/GenBank-update"\
TARGET=_blank>GenBank: update</A>.\
<em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D23-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681350" target="_blank">14681350</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308779/" target="_blank">PMC308779</a>\
</p>\
\
<P>\
Kent WJ.\
<A HREF="https://genome.cshlp.org/content/12/4/656.abstract" \
TARGET=_blank>BLAT - the BLAST-like alignment tool</A>.\
<em>Genome Res</em>. 2002 Apr;12(4):656-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a>\
</p>\
	rna	1	baseColorUseCds genbank\
baseColorUseSequence genbank\
group rna\
indelDoubleInsert on\
indelQueryInsert on\
longLabel Non-Mouse mRNAs from GenBank\
shortLabel Other mRNAs\
showDiffBasesAllScales .\
spectrum on\
track xenoMrna\
type psl xeno\
visibility hide\

wgEncodePsuDnaseViewPeaks	Peaks	bed 3	DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU\
parent wgEncodePsuDnase\
scoreFilter 100\
scoreFilterLimits 100:1000\
shortLabel Peaks\
track wgEncodePsuDnaseViewPeaks\
view Peaks\
visibility pack\

wgEncodePsuHistoneViewPeaks	Peaks	bed 3	Histone Modifications by ChIP-seq from ENCODE/PSU	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Histone Modifications by ChIP-seq from ENCODE/PSU\
pValueFilter 0\
pValueFilterLimits 0:320\
parent wgEncodePsuHistone\
qValueFilter 0\
qValueFilterLimits 0:320\
shortLabel Peaks\
signalFilter 0\
signalFilterLimits 0:18241\
track wgEncodePsuHistoneViewPeaks\
view Peaks\
visibility pack\

wgEncodeCaltechHistViewPeaks	Peaks	bed 3	Histone Modifications by ChIP-seq from ENCODE/Caltech	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Histone Modifications by ChIP-seq from ENCODE/Caltech\
minGrayLevel 5\
parent wgEncodeCaltechHist\
scoreFilter 0\
scoreFilterLimits 1:1000\
scoreMin 0\
shortLabel Peaks\
signalFilter 0\
signalFilterLimits 0:82\
track wgEncodeCaltechHistViewPeaks\
view Peaks\
visibility pack\

wgEncodeCaltechTfbsViewPeaks	Peaks	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech\
minGrayLevel 5\
parent wgEncodeCaltechTfbs\
scoreFilter 0\
scoreFilterLimits 1:1000\
scoreMin 0\
shortLabel Peaks\
signalFilter 0\
signalFilterLimits 0:82\
track wgEncodeCaltechTfbsViewPeaks\
view Peaks\
visibility pack\

wgEncodeLicrHistoneViewPeaks	Peaks	bed 3	Histone Mods by ChIP-seq from ENCODE/LICR	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Histone Mods by ChIP-seq from ENCODE/LICR\
parent wgEncodeLicrHistone\
scoreFilter 0\
scoreFilterLimits 1:1000\
scoreMin 0\
shortLabel Peaks\
signalFilter 0\
signalFilterLimits 0:125\
track wgEncodeLicrHistoneViewPeaks\
view Peaks\
visibility pack\

wgEncodeUwDnaseViewPeaks	Peaks	bed 3	DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington\
pValueFilter 0.0\
pValueFilterLimits 1:324\
parent wgEncodeUwDnase\
scoreFilter 10\
scoreFilterLimits 100:1000\
scoreMin 0\
shortLabel Peaks\
track wgEncodeUwDnaseViewPeaks\
view Peaks\
visibility pack\

wgEncodeLicrTfbsViewPeaks	Peaks	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR\
parent wgEncodeLicrTfbs\
scoreFilter 0\
scoreFilterLimits 1:1000\
scoreMin 0\
shortLabel Peaks\
signalFilter 0\
signalFilterLimits 0:82\
track wgEncodeLicrTfbsViewPeaks\
view Peaks\
visibility pack\

wgEncodeSydhHistViewPeaks	Peaks	bed 3	Histone Modifications by ChIP-seq from ENCODE/SYDH	1	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Histone Modifications by ChIP-seq from ENCODE/SYDH\
pValueFilter 2\
pValueFilterLimits 0:300\
parent wgEncodeSydhHist\
qValueFilter 2\
qValueFilterLimits 0:300\
shortLabel Peaks\
signalFilter 0\
signalFilterLimits 0:18241\
track wgEncodeSydhHistViewPeaks\
view Peaks\
visibility dense\

wgEncodeSydhTfbsViewPeaks	Peaks	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale\
pValueFilter 2\
pValueFilterLimits 0:300\
parent wgEncodeSydhTfbs\
qValueFilter 2\
qValueFilterLimits 0:300\
shortLabel Peaks\
signalFilter 0\
signalFilterLimits 0:18241\
track wgEncodeSydhTfbsViewPeaks\
view Peaks\
visibility pack\

wgEncodePsuTfbsViewPeaks	Peaks	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU	3	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU\
pValueFilter 0\
pValueFilterLimits 0:300\
parent wgEncodePsuTfbs\
qValueFilter 0\
qValueFilterLimits 0:300\
shortLabel Peaks\
signalFilter 0\
signalFilterLimits 0:18241\
track wgEncodePsuTfbsViewPeaks\
view Peaks\
visibility pack\

wgEncodeUwDgfViewPeaks	Peaks	bed 3	DNaseI Digital Genomic Footprinting from ENCODE/University of Washington	0	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel DNaseI Digital Genomic Footprinting from ENCODE/University of Washington\
minGrayLevel 3\
pValueFilter 0.0\
pValueFilterLimits 1:324\
parent wgEncodeUwDgf\
scoreFilter 100\
scoreFilterLimits 100:1000\
shortLabel Peaks\
track wgEncodeUwDgfViewPeaks\
view Peaks\
visibility hide\

ucscGenePfam	Pfam in UCSC Gene	bed 12	Pfam Domains in UCSC Genes	0	100	20	0	250	137	127	252	0	0	0		https://www.ebi.ac.uk/interpro/search/text/$$/?page=1#table	<h2>Description</h2>\
\
<p>\
Most proteins are composed of one or more conserved functional regions called\
domains. This track shows the high-quality, manually-curated\
<a href="http://pfam.xfam.org" target="_blank">\
Pfam-A</a>\
domains found in transcripts located in the UCSC Genes track by the software HMMER3.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track follows the display conventions for\
<a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene\
tracks</a>.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
The sequences from the knownGenePep table (see \
<a href="hgTrackUi?g=knownGene">UCSC Genes description page</a>)\
are submitted to the set of Pfam-A HMMs which annotate regions within the\
predicted peptide that are recognizable as Pfam protein domains. These regions\
are then mapped to the transcripts themselves using the\
<a href="http://hgdownload.soe.ucsc.edu/admin/exe/" target="_blank">\
pslMap utility</a>. A complete shell script log for every version of UCSC genes can be found in \
our GitHub repository under \
<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/ucscGenes/">hg/makeDb/doc/ucscGenes</a>,\
e.g. \
<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes17.csh#L1258">mm10.knownGenes17.csh</a>\
is for the database mm10 and version 17 of UCSC known genes.</p>\
\
<p>\
Of the several options for filtering out false positives, the &quot;Trusted cutoff (TC)&quot; \
threshold method is used in this track to determine significance. For more information regarding \
thresholds and scores, see the HMMER \
<a href="http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf#page=73" target="_blank">documentation</a> \
and \
<a href="https://hmmer-web-docs.readthedocs.io/en/latest/result.html#profile-hmm-matches" target="_blank">results interpretation</a> pages.\
</p>\
\
<p>\
Note: There is currently an undocumented but known HMMER problem which results in lessened \
sensitivity and possible missed searches for some zinc finger domains. Until a fix is released for \
HMMER /PFAM thresholds, please also consult the "UniProt Domains" subtrack of the UniProt track for \
more comprehensive zinc finger annotations.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
pslMap was written by Mark Diekhans at UCSC.\
</p>\
\
<h2>References</h2>\
\
<p>\
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G,\
Forslund K <em>et al</em>.\
<a href="https://academic.oup.com/nar/article/38/suppl_1/D211/3112325/The-Pfam-protein-families-\
database" target="_blank">The Pfam protein families database</a>.\
<em>Nucleic Acids Res</em>. 2010 Jan;38(Database issue):D211-22.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19920124" target="_blank">19920124</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808889/" target="_blank">PMC2808889</a>\
</p>\
	genes	1	color 20,0,250\
group genes\
longLabel Pfam Domains in UCSC Genes\
shortLabel Pfam in UCSC Gene\
track ucscGenePfam\
type bed 12\
url https://www.ebi.ac.uk/interpro/search/text/$$/?page=1#table\

wgEncodeCshlLongRnaSeqViewPlusRawSignal	Plus Raw Signal	bed 3	Long RNA-seq from ENCODE/Cold Spring Harbor Lab	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel Long RNA-seq from ENCODE/Cold Spring Harbor Lab\
maxHeightPixels 100:24:16\
minLimit 0\
parent wgEncodeCshlLongRnaSeq\
shortLabel Plus Raw Signal\
track wgEncodeCshlLongRnaSeqViewPlusRawSignal\
transformFunc NONE\
view PlusRawSignal\
viewLimits 1:100\
visibility full\
windowingFunction mean+whiskers\

wgEncodePsuRnaSeqViewPlusRawSignal	Plus Raw Signal	bed 3	RNA-seq from ENCODE/PSU	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
configurable on\
longLabel RNA-seq from ENCODE/PSU\
maxHeightPixels 100:50:16\
parent wgEncodePsuRnaSeq\
shortLabel Plus Raw Signal\
track wgEncodePsuRnaSeqViewPlusRawSignal\
transformFunc NONE\
view PlusRawSignal\
viewLimits 1:20000\
visibility full\
windowingFunction mean+whiskers\

polyASeqSites	PolyA-Seq	bed	Poly(A)-sequencing from Merck Research Laboratories	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
\
<p>\
This track displays the location of RNA polyadenylation (polyA) sites based\
on high-throughput RNA sequencing using the PolyA-seq protocol.\
</p>\
\
<p>\
PolyA-Seq data is strand-specific, therefore two tracks are provided for each tissue. PolyA\
site positions correspond to a single base, namely the ends of read alignments immediately\
upstream of the polyadenylation site. The data provided in this track consists of filtered\
polyA sites (see Methods). When multiple sites occurred within a 30-bp window on the same\
strand, the sum of the reads was attributed to the site with the most reads. Units are in\
reads per million (RPM) aligned. To obtain read counts, multiply RPM values by the total\
number of filtered reads for the corresponding experiment:\
</p>\
\
<table class="descTbl">\
<thead style="font-weight:bold;background-color:#FCECC0;">\
<tr> \
\	<th>Sample</th>\
\	<th>Filtered reads</th>\
</tr>\
</thead>\
<tbody>\
<tr>\
\	<td>Brain</td>\
\	<td>1187654</td>\
</tr>\
<tr>\
\	<td>Kidney</td>\
\	<td>3921370</td>\
</tr>\
<tr>\
\	<td>Liver</td>\
\	<td>4189409</td>\
</tr>\
<tr>\
\	<td>Muscle</td>\
\	<td>5517961</td>\
</tr>\
<tr>\
\	<td>Testis</td>\
\	<td>7466688</td>\
</tr>\
</tbody>\
</table>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
These tracks may be configured in a variety of ways to highlight different \
aspects of the displayed data. The graphical configuration options \
are shown at the top of the track description page.  For more information, \
see <a href="../goldenPath/help/hgWiggleTrackHelp.html" target="_blank">Configuring \
graph-based tracks</a>.\
</p>\
\
<p>\
In the full and pack display modes, forward-strand tracks are shown in <span style="color:#993333;">\
<b>red</b></span> and reverse-strand tracks are shown in <span\
style="color:#000;"><b>black</b></span>.\
In the squish and dense display modes, intensity is represented in grayscale (the darker\
the shading, the higher the intensity). To show only selected subtracks, uncheck the boxes next to\
the tracks that \
you wish to hide.\
</p>\
\
<h2>Methods</h2>\
\
<p>\
A detailed explanation of the experimental methods is provided at NCBI's Gene \
Expression Omnibus under accession <a\
href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30198" \
target=_blank>GSE30198</a>. Briefly, PolyA+ RNA was reverse-transcribed\
using a T(10)VN primer and strand-specific universal adapters, amplified, and sequenced\
on an Illumina GAIIx sequencer. Reads were reverse-complemented, aligned to the corresponding\
reference genome and splice junctions, and retained only if they aligned uniquely. 3' ends of\
alignments were considered polyA sites. Sites were then filtered using downstream base\
frequency matrices for true- and false-positive sites determined from a modified experiment \
based on a T(10) primer (i.e., excluding the 3' VN). When multiple filtered sites occurred\
within a 30-nt window on the same strand, read counts were summed and attributed to the most\
abundant peak. For each tissue, read counts were then divided by the total number of reads,\
in millions, from all filtered sites.\
</p>\
\
<h2>Credits</h2>\
\
<p>\
These data were generated at <a href="https://www.merck.com/mrl/" target="_blank">Merck Research\
Laboratories</a> and submitted by Adnan Derti and Tomas Babak.\
</p>\
\
<h2> Data Release Policy</h2>\
\
<p>No restrictions.</p>	rna	1	compositeTrack on\
dimensions dimensionY=tissType dimensionX=strand\
dragAndDrop subTracks\
group rna\
longLabel Poly(A)-sequencing from Merck Research Laboratories\
noInherit on\
shortLabel PolyA-Seq\
sortOrder tissType=+ strand=+ view=+\
subGroup1 view Views Signal=Signal\
subGroup2 tissType Tissue_Type Brain=Brain Kidney=Kidney Liver=Liver Muscle=Muscle Testis=Testis\
subGroup3 strand Strand fwd=Forward rev=Reverse\
track polyASeqSites\
type bed\
visibility hide\

wgEncodePsuDnase	PSU DNaseI HS	bed 3	DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P><DT><B><I>Rationale for the Mouse ENCODE project</I></B></DT>\
Knowledge of the function of genomic DNA sequences comes from three basic approaches. \
Genetics uses changes in behavior or structure of a cell or organism in response to changes in DNA sequence to infer function of the altered sequence. \
Biochemical approaches monitor states of histone modification, binding of specific transcription factors, accessibility to DNases and other epigenetic features along genomic DNA. \
In general, these features are associated with gene activity, but the precise relationships remain to be established. \
The third approach is evolutionary, using comparisons among homologous DNA sequences to find segments that are evolving more slowly or more rapidly than expected given the local rate of neutral change. \
Such changes are inferred to be under negative or positive selection, respectively, and interpreted as DNA sequences needed for a preserved (negative selection) or adaptive (positive selection) function.\
</p>\
<p>\
The ENCODE project aims to discover all the DNA sequences associated with various epigenetic features, with the reasonable expectation that these will also be functional \
(best tested by genetic methods). However, it is not clear how to relate these results with those from evolutionary analyses. \
The mouse ENCODE project aims to make this connection explicitly and with a moderate breadth. \
Assays identical to those being used in the ENCODE project are performed in cell types in mouse that are similar or homologous to those studied in the human project. \
The comparison will be used to discover which epigenetic features are conserved between mouse and human, and examine the extent to which these overlap with the DNA sequences under negative selection. \
The contribution of functional DNA preserved in mammals versus function in only one species will be discovered. The results will have a significant impact on the understanding of the evolution of gene regulation.\
</p>\
\
<P><DT><B><I>Maps of DNaseI Sensitivity</I></B></DT>\
DNaseI has long been used to map general chromatin accessibility, and DNaseI hypersensitivity \
is a universal feature of active cis-regulatory sequences.  Maps of DNaseI sensitivity measured genome-wide are generated through DNaseI digestion, addition of linkers at the sites of cleavage, \
and library prep followed by massively parallel short read sequencing on the Illumina GAIIx and HiSeq platforms. The sequence tags are mapped back to the mouse genome, and a graph of the \
smoothed kernel density of DNaseI cleavage sites is displayed as the "Signal" track. \
This provides a quantitative estimate of the frequency of cleavage by DNaseI in the initial digest, which in turn is related to the accessibility of the DNA in the chromatin. \
Segments of greatest cleavage site density represent DNase hypersensitive sites (DHSs) and are identified as peaks by the F-seq program (Boyle <em>et al.</em> 2008). DHSs are candidates for any cis-regulatory module, including promoters, enhancers, insulators, and novel elements. \
The sequence reads, quality scores, and alignment coordinates from these experiments are available for download.\
</p>\
\
<H2>Display Conventions and Configuration</H2>\
<p>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>). For each view, there are multiple subtracks that display\
individually on the browser. Instructions for configuring multi-view tracks\
are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
<DL>\
<DT><I>Peaks</I></DT>\
<DD> DNaseI hypersensitive sites (DHSs) identified as signal peaks.\
Peaks were called based on signals created using F-Seq, a software program developed at Duke (Boyle <em>et al.</em>, 2008). \
Significant regions were determined by fitting the data to a gamma distribution to calculate p-values. The solid vertical line in the peak represents the point with the highest signal.</DD>\
<DT><I>Signal</I></DT>\
<DD>Density graph (wiggle) of signal enrichment calculated using F-Seq for each replicate. \
F-Seq employs Parzen kernel density estimation to create base pair scores (Boyle <em>et al.</em>, 2008). \
This method does not look at fixed-length windows, but rather weights contributions of nearby sequences in proportion to their distance from that base. </DD>\
</DL>\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
\
\
<H2>Methods</H2>\
Cells were grown and harvested according to the approved <a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>\
for G1E and G1E-ER4. \
<p>\
DNaseI hypersensitive sites were isolated using methods called DNase-seq or DNase-chip (Song and Crawford, 2010). \
Briefly, cells were lysed with NP40, and intact nuclei were digested with optimal levels of DNaseI enzyme. \
DNaseI-digested ends were captured from three different DNase concentrations, and material was sequenced using Illumina sequencing.\
</p>\
\
<p>\
The read length for sequences from DNase-seq is 20 bases long due to a MmeI cutting step of the approximately 50 kb DNA fragments extracted after DNaseI digestion. \
Sequences from each experiment were mapped to the mouse genome (mm9 assembly) using the program\
<a href="http://bowtie-bio.sourceforge.net/index.shtml" target="_blank">Bowtie</a> (Langmead <em>et al.</em>, 2009).  \
Reads mapping to more than one location were not removed. For such reads, only the best mapping result was used ("--best" option).\
Sequences from multiple lanes were combined for a single replicate and converted to the sam/bam format using\
<a href="http://samtools.sourceforge.net/" target="_blank">SAMtools</a>.  \
Using F-seq, the resulting digital signal was converted to a continuous wiggle track that employs a Parzen kernel density estimation to create base pair scores (Boyle <em>et al.</em>, 2008).\
</p>\
\
<p>\
Discrete DNaseI HS sites (peaks) were identified from the DNase-seq F-seq density signal. Significant regions were determined by fitting the data to a gamma distribution to calculate p-values.\
</p>\
\
\
<H2>Credits</H2>\
<p>\
Cell growth and DNaseI digestion were done by Christine Dorman in the Hardison lab, and DNase-seq libraries were constructed in the laboratory of Greg Crawford (Duke).  \
Sequencing was done by the laboratory of Greg Crawford (Duke). Data processing and analysis was done by Chris Morrissey (PSU) and Yoichiro Shibata (Duke) with advice from Terry Furey (University of North Carolina). \
Some analyses used tools provided in the Galaxy platform (Anton Nekrutenko, PSU, and James Taylor, Emory) enabled by the Penn State Cyberstar computer (supported by the National Science Foundation). \
Generation of these data was supported by National Institutes of Health grants R01DK065806 and RC2HG005573.\
<p>\
\
<p>\
Contact:\
<A HREF="mailto:&#114;&#99;h&#56;&#64;&#112;&#115;&#117;.\
&#101;&#100;u"\
title="mailto:&#114;&#99;h&#56;&#64;&#112;&#115;&#117;.\
&#101;&#100;u" rel="nofollow"\
TARGET=_BLANK>Ross Hardison</A>\
<!-- above address is Ross Hardison at psu.edu -->\
</p>\
\
<H2>References</H2>\
<p>\
Boyle AP, Guinney J, Crawford GE, Furey TS.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18784119" target="_blank">\
F-Seq: a feature density estimator for high-throughput sequence tags</a>.\
<em>Bioinformatics</em>. 2008 Nov 1;24(21):2537-8.\
</p>\
\
<p>\
Langmead B, Trapnell C, Pop M, Salzberg SL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174" target="_blank">\
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>.\
<em>Genome Biol</em>. 2009;10(3):R25.\
</p>\
\
<p>\
Song L, Crawford GE.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20150147" target="_blank">\
DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome\
from mammalian cells</a>.\
<em>Cold Spring Harb Protoc</em>. 2010 Feb;2010(2):pdb.prot5384.\
</p>\
\
\
<h2>Publications</h2>\
<p>\
Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21795386" target="_blank">\
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration</a>.\
<em>Genome Res</em>. 2011 Oct;21(10):1659-71.\
</p>\
\
\
\
<H2> Data Release Policy </H2>\
\
<p>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column, above.  The full data release policy\
for ENCODE is available\
<A TARGET=_BLANK HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</p>\
\
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wgEncodePsuHistone	PSU Histone	bed 3	Histone Modifications by ChIP-seq from ENCODE/PSU	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<P><DT><B><I>Rationale for the Mouse ENCODE project</I></B></DT>\
Knowledge of the function of genomic DNA sequences comes from three \
basic approaches. Genetics uses changes in behavior or structure of a cell or organism\
in response to changes in DNA sequence to infer function of the altered sequence. \
Biochemical approaches monitor states of histone modification, binding of specific \
transcription factors, accessibility to DNases and other epigenetic features along \
genomic DNA. In general, these are associated with gene activity, but the precise \
relationships remain to be established. The third approach is evolutionary, using \
comparisons among homologous DNA sequences to find segments that are evolving \
more slowly or more rapidly than expected given the local rate of neutral change. These \
are inferred to be under negative or positive selection, respectively, and interpreted \
as DNA sequences needed for a preserved (negative selection) or adaptive \
(positive selection) function. </P>\
\
<P>The ENCODE project aims to discover all the DNA sequences associated with \
various epigenetic features, with the reasonable expectation that these will also be \
functional &#40;best tested by genetic methods&#41;. However, it is not clear how to relate these \
results with those from evolutionary analyses. The mouse ENCODE project aims to \
make this connection explicitly and with a moderate breadth. Assays identical to those \
being used in the ENCODE project are performed in cell types in mouse that are similar \
or homologous to those studied in the human project. The comparison will be used to discover\
which epigenetic features are conserved between mouse and human, and  \
examine the extent to which these overlap with the DNA sequences under negative \
selection. The contribution of functional DNA  preserved in mammals versus \
function in only one species will be discovered. The results will have a \
significant impact on the understanding of the evolution of gene regulation.\
</P>\
\
<P><DT><B><I>Maps of histone modifications</I></B></DT>\
Levels of five histone modifications were determined. \
Methylation of lysine 4 of histone H3 is associated with active chromatin, with monomethylation (H3K4me1) \
associated with enhancers and trimethylation (H3K4me3) associated with active promoters. \
Trimethylation of lysine 36 (H3K36me3) is associated with elongating RNA polymerase II. \
Two marks associated with repressed chromatin were also determined, trimethylation of lysine 27 of histone H3 (H3K27me3) which is \
deposited by Polycomb repressive complex 2, and trimethylation of lysine 9 of histone H3 (H3K9me3). \
Maps of genomic DNA in chromatin with these histone modifications are generated by ChIP-seq. \
This consists of two basic steps: chromatin immunoprecipitation (ChIP) is used to highly enrich \
genomic DNA for the segments bound by specific proteins (the antigens recognized by the antibodies) \
followed by massively parallel short read sequencing to tag the enriched DNA segments. Sequencing was done on the Illumina GAIIx and HiSeq. \
The sequence tags are mapped back to the mouse genome (&#40;Langmead <em>et al.</em>, 2009&#41;), \
and a graph of the enrichment for histone modifications are displayed as the "Signal" track (essentially the counts of mapped reads per interval) \
and the deduced probable binding sites from the MACS program (&#40;Zhang <em>et al.</em>, 2008&#41;) are shown in the "Peaks" track. \
Each experiment is associated with an input signal, which represents the control condition where immunoprecipitation with non-specific immunoglobulin was performed in the same cell type. \
The sequence reads, quality scores, and alignment coordinates from these experiments are available for download.\
</P>\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
<DL>\
<DT><I>Peaks</I></DT><DD> Regions of signal enrichment based on processed data\
(usually normalized data from pooled replicates). Intensity is represented in \
grayscale; the darker shading shows higher intensity (a solid vertical line\
in the peak region represents the point with the highest signal).\
ENCODE Peaks tables contain fields for statistical significance, including FDR\
(<a href="/goldenPath/help/qValue.html" target="_blank">qValue</a>).</DD>\
<DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based on\
processed data.</DD>\
</DL>\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
\
<H2>Methods</H2>\
\
<P>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
</P>\
<P>\
The chromatin immunoprecipitation followed published methods &#40;Welch <EM>et al.</EM>, 2004&#41;.\
Information on antibodies used is available via the hyperlinks in the &#34;Select\
subtracks&#34; menu. Samples passing initial quality thresholds &#40;enrichment and depletion \
for positive and negative controls &#45; if available &#45; by quantitative PCR of ChIP material&#41;\
are processed for library construction for Illumina sequencing, using the ChIP-seq \
Sample Preparation Kit purchased from Illumina. Starting with a 10 ng sample of ChIP \
DNA, DNA fragments were repaired to generate blunt ends and a single A nucleotide \
was added to each end. Double-stranded Illumina adaptors were ligated to the \
fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between \
250-350 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA \
HS Assay Kit. The DNA library was sequenced on the Illumina Genome Analyzer II \
sequencing system, and more recently on the HiSeq. Cluster generation, linearization, \
blocking and sequencing primer reagents were provided in the Illumina Cluster \
Amplification kits. All samples were determined as biological replicates except time \
course samples. The data displayed are from the pooled reads for all replicates, but \
individual replicates are available by download.\
</P>\
\
<P>\
The resulting 36-nucleotide sequence reads &#40;fastq files&#41; were moved to a data \
library in Galaxy, and the tools implemented in Galaxy were used for further processing \
via workflows &#40;Blankenberg <EM>et al.</EM>, 2010&#41;. The reads were mapped to the mouse genome \
&#40;mm9 assembly&#41; using the program bowtie &#40;Langmead <EM>et al.</EM>, 2009&#41;, and the files of \
mapped reads for the ChIP sample and from the &#34;input&#34; control &#40;no antibody&#41; were \
processed by MACs &#40;Zhang <EM>et al.</EM>, 2008&#41; to call peaks for occupancy by transcription \
factors, using the parameters mfold=15, bandwidth=125. Since, the signal for some histone \
modifications is not expected to be tightly localized &#40;compared to a transcription factor&#41;,\
peak calling programs may not be appropriate. Thus in addition, we provide wiggle \
tracks with tag counts for every 10 bp segment. Per-replicate\
alignments and sequences are available for download at\
<A HREF="../cgi-bin/hgFileUi?db=mm9&amp;g=wgEncodePsuHistone"\
 TARGET=_BLANK>downloads page</A>.\
</P>\
\
<h2>Release Notes</h2>\
\
<p>\
This is Release 2 (August 2012). It contains a total of 30 ChIP-seq experiments on Histone Modifications with the addition of 1 new\
experiment.\
</p>\
<p>\
Previous versions of files are available for download from the\
<a HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuHistone/"\
TARGET=_BLANK>FTP site</A>.\
</p>\
\
\
<H2>Credits</H2>\
\
<p>\
Cell growth, ChIP, and Illumina library construction were done primarily by Weisheng Wu, \
and sequencing on the Illumina platform was done largely by Cheryl Keller in the laboratory of \
Ross Hardison (PSU). Data processing and analysis were overseen by James Taylor (Emory University), \
using tools provided in the Galaxy platform (Anton Nekrutenko, PSU, and James Taylor, Emory) enabled \
by the Penn State Cyberstar computer (supported by the National Science Foundation). \
Generation of these data was supported by National Institutes of Health grants R01DK065806 and RC2HG005573.\
</p>\
<p>\
Contact:\
<A HREF="mailto:&#114;&#99;h&#56;&#64;&#112;&#115;&#117;.\
&#101;&#100;u"\
title="mailto:&#114;&#99;h&#56;&#64;&#112;&#115;&#117;.\
&#101;&#100;u" rel="nofollow"\
 TARGET=_BLANK>Ross Hardison</A>\
<!-- above address is Ross Hardison at psu.edu -->\
</p>\
\
<H2>References</H2>\
\
<p>\
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/16630819" target="_blank">\
A bivalent chromatin structure marks key developmental genes in embryonic stem cells</a>.\
<em>Cell</em>. 2006 Apr 21;125(2):315-26.\
</p>\
\
<p>\
Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A, Galaxy Team.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20562416" target="_blank">\
Manipulation of FASTQ data with Galaxy</a>.\
<em>Bioinformatics</em>. 2010 Jul 15;26(14):1783-5.\
</p>\
\
<p>\
ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guig&#243; R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17571346" target="_blank">\
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project</a>.\
<em>Nature</em>. 2007 Jun 14;447(7146):799-816.\
</p>\
\
<p>\
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17277777" target="_blank">\
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome</a>.\
<em>Nat Genet</em>. 2007 Mar;39(3):311-8.\
</p>\
\
<p>\
Langmead B, Trapnell C, Pop M, Salzberg SL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174" target="_blank">\
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>.\
<em>Genome Biol</em>. 2009;10(3):R25.\
</p>\
\
<p>\
M&#252;ller J, Hart CM, Francis NJ, Vargas ML, Sengupta A, Wild B, Miller EL, O'Connor MB, Kingston RE, Simon JA.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/12408864" target="_blank">\
Histone methyltransferase activity of a Drosophila Polycomb group repressor complex</a>.\
<em>Cell</em>. 2002 Oct 18;111(2):197-208.\
</p>\
\
<p>\
Rando OJ, Chang HY.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19317649" target="_blank">\
Genome-wide views of chromatin structure</a>.\
<em>Annu Rev Biochem</em>. 2009;78:245-71.\
</p>\
\
<p>\
Weiss MJ, Yu C, Orkin SH.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/9032291" target="_blank">\
Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a gene-targeted cell line</a>.\
<em>Mol Cell Biol</em>. 1997 Mar;17(3):1642-51.\
</p>\
\
<p>\
Welch JJ, Watts JA, Vakoc CR, Yao Y, Wang H, Hardison RC, Blobel GA, Chodosh LA, Weiss MJ.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/15297311" target="_blank">\
Global regulation of erythroid gene expression by transcription factor GATA-1</a>.\
<em>Blood</em>. 2004 Nov 15;104(10):3136-47.\
</p>\
\
<p>\
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18798982" target="_blank">\
Model-based analysis of ChIP-Seq (MACS)</a>.\
<em>Genome Biol</em>. 2008;9(9):R137.\
</p>\
\
<h2>Publications</h2>\
\
<p>\
Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21795386" target="_blank">\
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration</a>.\
<em>Genome Res</em>. 2011 Oct;21(10):1659-71.\
</p>\
\
<H2>Data Release Policy</H2>\
\
<P>\
Data users may freely use ENCODE data, but may not, without prior consent, \
submit publications that use an unpublished ENCODE dataset until nine months \
following the release of the dataset. This date is listed in the <em>Restricted Until</em> column, \
above. The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
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wgEncodePsuRnaSeq	PSU RNA-seq	bed 3	RNA-seq from ENCODE/PSU	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<P><DT><B><I>Rationale for the Mouse ENCODE project</I></B></DT>\
Knowledge of the function of genomic DNA sequences comes from three \
basic approaches. Genetics uses changes in behavior or structure of a cell or organism\
in response to changes in DNA sequence to infer function of the altered sequence. \
Biochemical approaches monitor states of histone modification, binding of specific \
transcription factors, accessibility to DNases and other epigenetic features along \
genomic DNA. In general, these are associated with gene activity, but the precise \
relationships remain to be established. The third approach is evolutionary, using \
comparisons among homologous DNA sequences to find segments that are evolving \
more slowly or more rapidly than expected given the local rate of neutral change. These \
are inferred to be under negative or positive selection, respectively, and interpreted \
as DNA sequences needed for a preserved (negative selection) or adaptive \
(positive selection) function. </P>\
\
<P>The ENCODE project aims to discover all the DNA sequences associated with \
various epigenetic features, with the reasonable expectation that these will also be \
functional &#40;best tested by genetic methods&#41;. However, it is not clear how to relate these \
results with those from evolutionary analyses. The mouse ENCODE project aims to \
make this connection explicitly and with a moderate breadth. Assays identical to those \
being used in the ENCODE project are performed in cell types in mouse that are similar \
or homologous to those studied in the human project. Thus we will be able to discover which epigenetic \
features are conserved between mouse and human, and we can examine the extent to which \
these overlap with the DNA sequences under negative selection. \
The contribution of DNA with a function preserved in mammals versus that with a function \
in only one species will be discovered. \
</P>\
\
<p><DT><B><I>Transcriptome Maps</I></B></DT>\
One of the epigenetic features most closely related to genomic activity is the \
production of stable RNA, including transcripts from both protein-coding genes and noncoding transcripts. \
These genomic compilations of transcripts, or transcriptomes, are primary determinants \
of the way cells function, respond and differentiate, both by the production of proteins \
translated from coding transcripts and the regulatory activity of untranslated non-coding transcripts.\
Non-coding RNA's regulate gene expression through diverse mechanisms ranging from reducing \
chromatin accessibility &#40;affecting large regions or whole chromosomes&#41; to precise fine-tuning \
of transcription from specific genes, <em>e.g.</em> via RNAi. \
</p>\
\
<p>\
Even though a large proportion of mammalian genomes is transcribed, many of the transcribed segments have yet \
to be assigned any function. The ENCODE project aims to create a comprehensive, quantitative annotation \
of the human transcriptome in several cell and tissue types as well as to understand regulation of \
transcriptomes by establishing the relationship between regulatory factors and their targets. \
Mapping the mouse transcriptome in similar tissues will allow us to discern conservation of \
transcriptome profiles between mouse and human and to discover species-specific transcription patterns, \
and to infer conserved versus species-specific regulatory mechanisms. \
The results will have a significant impact on our understanding of the evolution of gene regulation.\
</p>\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
<DL>\
<DT><I>Raw Signals</I><DD>The Plus Raw Signal and Minus Raw Signal views show the density of mapped reads \
on the plus and minus strands (wiggle format), respectively.<DD>\
<DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based\
on processed data.</DD>\
<DT><I>Alignments</I></DT><DD>Mappings of short reads to the genome. <DD>\
</DL>\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
\
<H2>Methods</H2>\
\
<P>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
<p>\
Total RNA was extracted from 5-10 million cells using TRIzol reagent. \
This was followed by mRNA selection, fragmentation and cDNA synthesis, which were performed as described previously &#40;Mortazavi <em> et al.</em>, 2009&#41;. \
Double-stranded cDNA samples were processed for library construction for Illumina sequencing, using the Illumina ChIP-seq\
Sample Preparation Kit.\
</p>\
<p>\
Strand-specific libraries were generated in a similar manner, \
except for a couple of modifications described previously &#40;Parkhomchuk<em> et al.</em>, 2009&#41;. \
Briefly, instead of dTTP, dUTP was used during second-strand cDNA synthesis to label the second-strand cDNA.\
During library preparation, the dUTP-labeled cDNA was treated with Uracil N Glycosylase, prior to the PCR amplification step. \
This was done to remove uracil from the second-strand, following which the DNA was subjected to high heat to facilitate abasic scission of the second strand.\
</p>\
\
<p>\
Cluster generation, linearization, blocking and sequencing primer reagents were provided in the Illumina Cluster Amplification kits. \
All samples are considered as biological replicates.\
</p>\
\
<P>\
Sequencing was done on the Illumina Genome Analyzer IIx and on the Illumina HiSeq 2000. FastQ files for the resulting sequence reads (single read and paired-end, directional and non-directional)\
were moved to a data library in Galaxy, and tools implemented in Galaxy were used for further processing via workflows (&#40;Giardine <em>et al.</em>, 2005&#41;, &#40;Blankenberg <em> et al.</em>, 2010 &#41;, &#40;Goecks <em>et al.</em>, 2010&#41;).\
Data processing was also performed on the CyberSTAR high-performance computing system at Penn State. \
The reads were mapped to the mouse genome (mm9 assembly) using the program TopHat (&#40;Langmead <em>et al.</em>, 2009&#41; and &#40;Trapnell <em>et al.</em>, 2009&#41;). \
Signal tracks were created using BEDtools (Quinlan <em>et al.</em>, 2010) and SAMtools (Li, Handasaker <em>et al.</em>, 2009).\
</P>\
<H2>Credits</H2>\
<p>\
Cell growth and RNA isolation were done in the laboratories of Ross Hardison, Robert Paulson, David Bodine and Mitchell J. Weiss (PSU, NHGRI and Children's Hospital of Philadelphia). \
Isolation of mRNA, cDNA synthesis and Illumina library construction were done primarily by Tejaswini Mishra, \
and sequencing on the Illumina was done largely by Cheryl Keller, both in the laboratory of Ross Hardison.\
Mapping and transcript assembly were done by Belinda Giardine and Tejaswini Mishra on Galaxy and the CyberSTAR, Penn State high-performance computing system. \
Data processing and analysis were overseen by James Taylor (Emory University) and Ross Hardison (PSU). \
Generation of these data was supported by National Institutes of Health grants R01DK065806 and RC2HG005573. This work was supported in part through instrumentation funded by the National Science Foundation through grant OCI-0821527.  \
</p>\
\
<p>\
Contact:\
<A HREF="mailto:&#114;&#99;h&#56;&#64;&#112;&#115;&#117;.\
&#101;&#100;u"\
title="mailto:&#114;&#99;h&#56;&#64;&#112;&#115;&#117;.\
&#101;&#100;u" rel="nofollow"\
 TARGET=_BLANK>Ross Hardison</A>\
<!-- above address is Ross Hardison at psu.edu -->\
</p>\
\
<H2>References</H2>\
\
<p>\
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20069535" target="_blank">\
Galaxy: a web-based genome analysis tool for experimentalists</a>.\
<em>Curr Protoc Mol Biol</em>. 2010 Jan;Chapter 19:Unit 19.10.1-21.\
</p>\
\
<p>\
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/16169926" target="_blank">\
Galaxy: a platform for interactive large-scale genome analysis</a>.\
<em>Genome Res</em>. 2005 Oct;15(10):1451-5.\
</p>\
\
<p>\
Goecks J, Nekrutenko A, Taylor J, Galaxy Team.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20738864" target="_blank">\
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent\
computational research in the life sciences</a>.\
<em>Genome Biol</em>. 2010;11(8):R86.\
</p>\
\
<p>\
Langmead B, Trapnell C, Pop M, Salzberg SL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174" target="_blank">\
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>.\
<em>Genome Biol</em>. 2009;10(3):R25.\
</p>\
\
<p>\
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome\
Project Data Processing Subgroup.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19505943" target="_blank">\
The Sequence Alignment/Map format and SAMtools</a>.\
<em>Bioinformatics</em>. 2009 Aug 15;25(16):2078-9.\
</p>\
\
<p>\
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18516045" target="_blank">\
Mapping and quantifying mammalian transcriptomes by RNA-Seq</a>.\
<em>Nat Methods</em>. 2008 Jul;5(7):621-8.\
</p>\
\
<p>\
Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19620212" target="_blank">\
Transcriptome analysis by strand-specific sequencing of complementary DNA</a>.\
<em>Nucleic Acids Res</em>. 2009 Oct;37(18):e123.\
</p>\
\
<p>\
Quinlan AR, Hall IM.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20110278" target="_blank">\
BEDTools: a flexible suite of utilities for comparing genomic features</a>.\
<em>Bioinformatics</em>. 2010 Mar 15;26(6):841-2.\
</p>\
\
<p>\
Trapnell C, Pachter L, Salzberg SL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19289445" target="_blank">\
TopHat: discovering splice junctions with RNA-Seq</a>.\
<em>Bioinformatics</em>. 2009 May 1;25(9):1105-11.\
</p>\
\
\
<H2>Data Release Policy</H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column on the track configuration page and\
the download page.  The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
	regulation	1	compositeTrack on\
controlledVocabulary encode/cv.ra cellType=cell strain=strain sex=sex treatment=treatment age=age\
dimensionAchecked R1X41,R1X45,R1X55,R2X99D\
dimensions dimensionX=cellType dimensionY=rep dimensionZ=treatment dimensionA=readType\
dragAndDrop subTracks\
fileSortOrder cell=Cell_Line treatment=Treatment readType=Read-Type replicate=Replicate view=View dccAccession=UCSC_Accession geoSampleAccession=GEO_Sample<BR>Accession fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until\
filterComposite dimZ=all dimA=multi\
group regulation\
longLabel RNA-seq from ENCODE/PSU\
noInherit on\
priority 0\
shortLabel PSU RNA-seq\
sortOrder cellType=+ treatment=+ readType=+ rep=+ view=-\
subGroup1 view Views Signal=Signal MinusRawSignal=Minus_Raw_Signal PlusRawSignal=Plus_Raw_Signal Alignments=Alignments\
subGroup2 cellType Cell_Line CH12=CH12 ERYTHROBL=Erythroblast FVP=FV-progenitor FVLS=FVL-stem G1E=G1E G1EER4=G1E-ER4 G1EER4T=G1E-ER4&nbsp;(Time_Course) MEGAKARYO=Megakaryocyte MEL=MEL MEP=MEP\
subGroup3 sex Sex F=F M=M U=U B=B\
subGroup4 age Age E0=E0 E14HALF=E14.5 IMMORTAL=immortalized ADULT810WKS=adult-10-12wks ADULT5WKS=adult-5wks\
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subGroup6 readType ReadType R1X36=1x36  R1X41=1x41 R1X45=1x45 R1X55=1x55 R2X99D=2x99D\
subGroup7 treatment Treatment aNONE=None bDM2P5D=DMSO_2.0pct cDIFFD3H=Estradiol_3hr dDIFFD7H=Estradiol_7hr eDIFFD14H=Estradiol_14hr fDIFFD24H=Estradiol_24hr gDIFFD30H=Estradiol_30hr\
subGroup8 rep Replicate rep1=1 rep2=2\
track wgEncodePsuRnaSeq\
type bed 3\

wgEncodePsuTfbs	PSU TFBS	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<P><DT><B><I>Rationale for the Mouse ENCODE project</I></B></DT>\
Knowledge of the function of genomic DNA sequences comes from three \
basic approaches. Genetics uses changes in behavior or structure of a cell or organism\
in response to changes in DNA sequence to infer function of the altered sequence. \
Biochemical approaches monitor states of histone modification, binding of specific \
transcription factors, accessibility to DNases and other epigenetic features along \
genomic DNA. In general, these are associated with gene activity, but the precise \
relationships remain to be established. The third approach is evolutionary, using \
comparisons among homologous DNA sequences to find segments that are evolving \
more slowly or more rapidly than expected given the local rate of neutral change. These \
are inferred to be under negative or positive selection, respectively, and interpreted \
as DNA sequences needed for a preserved (negative selection) or adaptive \
(positive selection) function. </P>\
\
<P>The ENCODE project aims to discover all the DNA sequences associated with \
various epigenetic features, with the reasonable expectation that these will also be \
functional &#40;best tested by genetic methods&#41;. However, it is not clear how to relate these \
results with those from evolutionary analyses. The mouse ENCODE project aims to \
make this connection explicitly and with a moderate breadth. Assays identical to those \
being used in the ENCODE project are performed in cell types in mouse that are similar \
or homologous to those studied in the human project. The comparison will be used to discover \
which epigenetic features are conserved between mouse and human, and  \
examine the extent to which these overlap with the DNA sequences under negative \
selection. The contribution of functional DNA preserved in mammals versus \
function with in only one species will be discovered. The results will have a \
significant impact on the understanding of the evolution of gene regulation.\
</P>\
\
<P><DT><B><I>Maps of Occupancy by Transcription Factors</I></B></DT>\
Maps of occupancy of genomic DNA by transcription factors &#40;TFs&#41; are determined by \
ChIP-seq. This consists of two basic steps: chromatin immunoprecipitation &#40;ChIP&#41; is \
used to highly enrich genomic DNA for the segments bound by specific proteins &#40;the \
antigens recognized by the antibodies&#41; followed by massively parallel short read \
sequencing to tag the enriched DNA segments. Sequencing is done on the Illumina \
GAIIx and HiSeq. The sequence tags are mapped back to the mouse genome \
&#40;Langmead <EM>et al.</EM> 2009&#41;, and a graph of the enrichment for TF binding are displayed as \
the &#34;Signal&#34; track &#40;essentially the counts of mapped reads per interval&#41; and the deduced \
probable binding sites from the MACS program &#40;Zhang <EM>et al.</EM> 2008&#41; are shown in the \
&#34;Peaks&#34; track. Each experiment is associated with an input signal, which represents the \
control condition where immunoprecipitation with non-specific immunoglobulin was \
performed in the same cell type. The sequence reads, quality scores, and alignment \
coordinates from these experiments are available for download. </P>\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
<DL>\
<DT><I>Peaks</I></DT><DD> Regions of signal enrichment based on processed data\
(usually normalized data from pooled replicates). Intensity is represented in \
grayscale; the darker shading shows higher intensity (a solid vertical line\
in the peak region represents the point with the highest signal).\
ENCODE Peaks tables contain fields for statistical significance, including FDR\
(<a href="/goldenPath/help/qValue.html" target="_blank">qValue</a>).</DD>\
<DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based on\
processed data.</DD>\
</DL>\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
\
<H2>Methods</H2>\
\
<P>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
</P>\
<P>\
The chromatin immunoprecipitation followed published methods &#40;Welch <EM>et al.</EM> 2004&#41;.\
Information on antibodies used is available via the hyperlinks in the &#34;Select\
subtracks&#34; menu. Samples passing initial quality thresholds &#40;enrichment and depletion \
for positive and negative controls &#45; if available &#45; by quantitative PCR of ChIP material&#41;\
are processed for library construction for Illumina sequencing, using the ChIP-seq \
Sample Preparation Kit purchased from Illumina. Starting with a 10 ng sample of ChIP \
DNA, DNA fragments were repaired to generate blunt ends and a single A nucleotide \
was added to each end. Double-stranded Illumina adaptors were ligated to the \
fragments. Ligation products were amplified by 18 cycles of PCR, and the DNA between \
250-350 bp was gel purified. Completed libraries were quantified with Quant-iT dsDNA \
HS Assay Kit. The DNA library was sequenced on the Illumina Genome Analyzer II \
sequencing system, and more recently on the HiSeq. Cluster generation, linearization, \
blocking and sequencing primer reagents were provided in the Illumina Cluster \
Amplification kits. All samples were determined as biological replicates except time \
course samples. The data displayed are from the pooled reads for all replicates, but \
individual replicates are available by download.\
</P>\
\
<P>\
The resulting 36-nucleotide sequence reads &#40;fastq files&#41; were moved to a data \
library in Galaxy, and the tools implemented in Galaxy were used for further processing \
via workflows &#40;Blankenberg <EM>et al.</EM> 2010&#41;. The reads were mapped to the mouse genome \
&#40;mm9 assembly&#41; using the program bowtie &#40;Langmead <EM>et al.</EM> 2009&#41;, and the files of \
mapped reads for the ChIP sample and from the &#34;input&#34; control &#40;no antibody&#41; were \
processed by MACs &#40;Zhang <EM>et al.</EM> 2008&#41; to call peaks for occupancy by transcription \
factors, using the parameters mfold=15, bandwidth=125.  Per-replicate\
alignments and sequences are available for download at\
<A HREF="../cgi-bin/hgFileUi?db=mm9&amp;g=wgEncodePsuTfbs"\
 TARGET=_BLANK>downloads page</A>.\
</P>\
\
<h2>Release Notes</h2>\
\
<p>\
This is Release 2 (August 2012). It contains a total of 38 ChIP-seq experiments on Transcription Factor Binding Sites with the addition of 14 new\
experiments.\
</p>\
<p>\
One data set added an additional replicate: Megakaryocyte/GATA1_(SC-265) (UCSC Accession: wgEncodeEM002351).\
Files that have been reanalyzed have a version number appended to the name, <i>e.g.</i>V2.\
</p>\
<p>\
Previous versions of files are available for download from the\
<a HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodePsuTfbs/"\
TARGET=_BLANK>FTP site</A>.\
</p>\
\
\
<H2>Credits</H2>\
\
<p>\
Cell growth, ChIP, and Illumina library construction were done by researchers in the laboratories of Ross Hardison (PSU), Gerd Blobel and Mitch Weiss (Children's Hospital of Philadelphia); \
major contributors include Yong Cheng, Weisheng Wu, Deepti Jain, Cheryl Keller, Swathi Ashok Kumar, Tejaswini Mishra, Marta Byrska-Bishop, \
Stephan Kadauke, Maheshi Udugama, and Rena Zheng. Sequencing on the Illumina platform was done largely by Cheryl Keller in the laboratory of Ross Hardison (PSU). \
Data processing and analysis had major input from Chris Morrissey, Dan Blankenberg, and Belinda Giardine, as overseen by James Taylor (Emory University) and using tools provided in the Galaxy platform (Anton Nekrutenko, PSU, and James Taylor, Emory) \
enabled by the Penn State Cyberstar computer (supported by the National Science Foundation). Generation of these data was supported by National Institutes of Health grants R01DK065806 and RC2HG005573.\
</p>\
<p>\
Contact:\
<A HREF="mailto:&#114;&#99;h&#56;&#64;&#112;&#115;&#117;.\
&#101;&#100;u"\
title="mailto:&#114;&#99;h&#56;&#64;&#112;&#115;&#117;.\
&#101;&#100;u" rel="nofollow"\
 TARGET=_BLANK>Ross Hardison</A>\
<!-- above address is Ross Hardison at psu.edu -->\
</p>\
\
<H2>References</H2>\
\
<p>\
Aplan PD, Nakahara K, Orkin SH, Kirsch IR.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/1396592" target="_blank">\
The SCL gene product: a positive regulator of erythroid differentiation</a>.\
<em>EMBO J</em>. 1992 Nov;11(11):4073-81.\
</p>\
\
<p>\
Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A, Galaxy Team.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/20562416" target="_blank">\
Manipulation of FASTQ data with Galaxy</a>.\
<em>Bioinformatics</em>. 2010 Jul 15;26(14):1783-5.\
</p>\
\
\
<p>\
Green AR, DeLuca E, Begley CG.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/1756722" target="_blank">\
Antisense SCL suppresses self-renewal and enhances spontaneous erythroid differentiation of the\
human leukaemic cell line K562</a>.\
<em>EMBO J</em>. 1991 Dec;10(13):4153-8.\
</p>\
\
<p>\
Huang S, Brandt SJ.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/10688671" target="_blank">\
mSin3A regulates murine erythroleukemia cell differentiation through association with the TAL1 (or\
\	\	SCL) transcription factor</a>.\
<em>Mol Cell Biol</em>. 2000 Mar;20(6):2248-59.\
</p>\
\
<p>\
Huang S, Qiu Y, Shi Y, Xu Z, Brandt SJ.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/11118214" target="_blank">\
P/CAF-mediated acetylation regulates the function of the basic helix-loop-helix transcription factor\
TAL1/SCL</a>.\
<em>EMBO J</em>. 2000 Dec 15;19(24):6792-803.\
</p>\
\
\
<p>\
Langmead B, Trapnell C, Pop M, Salzberg SL.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19261174" target="_blank">\
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome</a>.\
<em>Genome Biol</em>. 2009;10(3):R25.\
</p>\
\
<p>\
Shivdasani RA, Mayer EL, Orkin SH.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/7830794" target="_blank">\
Absence of blood formation in mice lacking the T-cell leukaemia oncoprotein tal-1/SCL</a>.\
<em>Nature</em>. 1995 Feb 2;373(6513):432-4.\
</p>\
\
<p>\
Tripic T, Deng W, Cheng Y, Zhang Y, Vakoc CR, Gregory GD, Hardison RC, Blobel GA.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19011221" target="_blank">\
SCL and associated proteins distinguish active from repressive GATA transcription factor\
complexes</a>.\
<em>Blood</em>. 2009 Mar 5;113(10):2191-201.\
</p>\
\
\
<p>\
Wadman IA, Osada H, Gr&#252;tz GG, Agulnick AD, Westphal H, Forster A, Rabbitts TH.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/9214632" target="_blank">\
The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which\
includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins</a>.\
<em>EMBO J</em>. 1997 Jun 2;16(11):3145-57.\
</p>\
\
<p>\
Weiss MJ, Yu C, Orkin SH.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/9032291" target="_blank">\
Erythroid-cell-specific properties of transcription factor GATA-1 revealed by phenotypic rescue of a\
gene-targeted cell line</a>.\
<em>Mol Cell Biol</em>. 1997 Mar;17(3):1642-51.\
</p>\
\
<p>\
Welch JJ, Watts JA, Vakoc CR, Yao Y, Wang H, Hardison RC, Blobel GA, Chodosh LA, Weiss MJ.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/15297311" target="_blank">\
Global regulation of erythroid gene expression by transcription factor GATA-1</a>.\
<em>Blood</em>. 2004 Nov 15;104(10):3136-47.\
</p>\
\
<p>\
Wold B, Myers RM.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18165803" target="_blank">\
Sequence census methods for functional genomics</a>.\
<em>Nat Methods</em>. 2008 Jan;5(1):19-21.\
</p>\
\
<p>\
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W\
<em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/18798982" target="_blank">\
Model-based analysis of ChIP-Seq (MACS)</a>.\
<em>Genome Biol</em>. 2008;9(9):R137.\
</p>\
\
<h2>Publications</h2>\
\
<p>\
Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21795386" target="_blank">\
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration</a>.\
<em>Genome Res</em>. 2011 Oct;21(10):1659-71.\
</p>\
\
<H2>Data Release Policy</H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column on the track configuration page and\
the download page.  The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
	regulation	1	compositeTrack on\
controlledVocabulary encode/cv.ra cellType=cell factor=antibody treatment=treatment sex=sex age=age strain=strain control=control\
dimensions dimensionX=cellType dimensionY=factor dimensionA=treatment\
dragAndDrop subTracks\
fileSortOrder cell=Cell_Line treatment=Treatment antibody=Antibody<BR>Target labExpId=Lab_ID replicate=Replicate view=View controlId=Control_ID dccAccession=UCSC_Accession geoSampleAccession=GEO_Sample<BR>Accession fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until\
filterComposite dimA=all\
group regulation\
html wgEncodePsuTfbs.release2\
longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU\
noInherit on\
priority 0\
shortLabel PSU TFBS\
sortOrder cellType=+ treatment=+ factor=+ rep=+ view=+\
subGroup1 view Views Peaks=Peaks Signal=Signal\
subGroup2 cellType Cell_Line CH12=CH12 ERYTHROBL=Erythroblast G1E=G1E G1EER4=G1E-ER4 G1EER4T=G1E-ER4&nbsp;(Time_Course) MEGAKARYO=Megakaryocyte MEL=MEL\
subGroup3 factor Factor CTCF=CTCF GATA1a=GATA1_(SC-265) GATA2SC9008=GATA2_(SC-9008) FLI1SC356=FLI1_(SC-356) PAX5c=PAX5_(N-15) POL24H8=Pol2-4H8  TAL1=TAL1_(SC-12984) zINPUT=Input\
subGroup4 sex Sex B=B F=F M=M U=U\
subGroup5 age Age IMMORTAL=immortalized E0=E0 E14HALF=E14.5\
subGroup6 strain Strain s2A4B=B10.H-2aH-4bp/Wts s129=129 C57BL6=C57BL/6 CD1=CD-1 UKN=Unknown\
subGroup7 control Control INPUT=Input\
subGroup8 treatment Treatment aNONE=None bDIFFD3H=Estradiol_3hr cDIFFD7H=Estradiol_7hr dDIFFD14H=Estradiol_14hr eDIFFD24H=Estradiol_24hr fDIFFD30H=Estradiol_30hr\
subGroup9 rep Replicate rep1=1 repP=Pooled\
track wgEncodePsuTfbs\
type bed 3\
visibilityViewDefaults Peaks=pack Signal=full\

wgEncodeCaltechRnaSeqViewRawSignal	RawSignal	bed 3	RNA-seq from ENCODE/Caltech	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale on\
longLabel RNA-seq from ENCODE/Caltech\
maxHeightPixels 100:24:16\
parent wgEncodeCaltechRnaSeq\
shortLabel RawSignal\
track wgEncodeCaltechRnaSeqViewRawSignal\
transformFunc NONE\
view RawSignal\
viewLimits 0:500\
visibility full\
windowingFunction mean+whiskers\

wgEncodeUwDgfViewRawSignal	RawSignal	bed 3	DNaseI Digital Genomic Footprinting from ENCODE/University of Washington	0	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel DNaseI Digital Genomic Footprinting from ENCODE/University of Washington\
maxHeightPixels 100:32:16\
maxLimit 218367.00\
minLimit 1\
parent wgEncodeUwDgf\
shortLabel RawSignal\
track wgEncodeUwDgfViewRawSignal\
view RawSignal\
viewLimits 1:250\
visibility hide\
windowingFunction mean+whiskers\

rest	REST	bed 4 .	Repressor Element 1-Silencing Transcription Factor (REST) binding sites	0	100	0	0	200	255	0	0	0	0	0			\
<H2>Description</H2>\
<P>\
This track contains genome-wide maps of Repressor Element 1-Silencing \
Transcription Factor (REST) binding sites in mouse stem cells, generated \
by the Stem Cell and Developmental Biology Group at the \
Genome Institute of Singapore. \
REST is a zinc finger transcriptional repressor that regulates a large \
cohort of neural genes throughout development. Aberrant REST activity \
has been implicated in various disease states, including cancer, epilepsy, \
Huntington's disease and cardiovascular disease.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<ul>\
<li>The Embryonic Stem Cells only PET clusters (marked: ESC_only) \
are colored <span style="color: red;">red</span>.</li>\
<li>The Embryonic and Neural Stem Cells PET clusters (marked: ESC_NSC)\
are colored <span style="color: blue;">blue</span>.</li>\
</ul>\
\
<H2>Methods</H2>\
<P>\
The ChIP-PET (chromatin immunoprecipitation coupled to paired-end di-tagging) \
method was used to identify genomic loci occupied by REST. 36 bp PETs \
generated from ChIP DNA fragments enriched for REST binding regions were \
sequenced using the high-throughput 454 sequencing technology. \
REST binding sites were defined as those having at least five overlapping \
PETs (PET5+). Mapping was carried out in two isogenic cell lines: \
the mouse embyronic stem cell E14, and the neural stem cell line NS5. \
The REST binding sites are divided into two categories: \
<UL>\
 <LI>ESC and NSC shared sites, "ESC_NSC" (PET5+ in ESC, PET2+ in NSC)\
 <LI>ESC-specific sites, "ESC_only" (PET5+ in ESC, PET&lt;2 in NSC)\
</UL>\
Negligible numbers of NS-only sites were identified. The coordinates \
displayed represent the PET minimal overlap region, defined as the region \
that is overlapped in common by all PETs constituting a cluster.\
</P>\
<H2>Credits</H2>\
<P>\
These data were generated by the \
<A\
HREF="http://www.gis.a-star.edu.sg/internet/site/investigator/investigator.php?user_id=27" \
TARGET=_blank>Stanton Group</A> at the \
<A HREF="https://www.a-star.edu.sg/gis" \
TARGET=_blank>Genome Institute of Singapore</A>.\
</P>\
\
<H2>References</H2>\
<p>\
Johnson R, Teh CH, Kunarso G, Wong KY, Srinivasan G, Cooper ML, Volta M, Chan SS, Lipovich L,\
Pollard SM <em>et al</em>.\
<a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060256"\
target="_blank">REST regulates distinct transcriptional networks in embryonic and neural stem\
cells</a>. <em>PLoS Biol</em>. 2008 Oct 28;6(10):e256.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18959480" target="_blank">18959480</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2573930/" target="_blank">PMC2573930</a>\
</p>\
	regulation	1	altColor 255,0,0\
color 0,0,200\
group regulation\
longLabel Repressor Element 1-Silencing Transcription Factor (REST) binding sites\
shortLabel REST\
track rest\
type bed 4 .\
visibility hide\

genomicSuperDups	Segmental Dups	bed 6 +	Duplications of >1000 Bases of Non-RepeatMasked Sequence	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions detected as putative genomic duplications within the\
golden path. The following display conventions are used to distinguish\
levels of similarity:\
<UL>\
<LI>\
Light to dark gray: 90 - 98% similarity\
<LI>\
Light to dark yellow: 98 - 99% similarity\
<LI>\
Light to dark orange: greater than 99% similarity \
<LI>\
Red: duplications of greater than 98% similarity that lack sufficient \
Segmental Duplication Database evidence (most likely missed overlaps) \
</UL>\
For a region to be included in the track, at least 1 Kb of the total \
sequence (containing at least 500 bp of non-RepeatMasked sequence) had to \
align and a sequence identity of at least 90% was required.</P>\
\
<H2>Methods</H2>\
<P>\
Segmental duplications play an important role in both genomic disease \
and gene evolution.  This track displays an analysis of the global \
organization of these long-range segments of identity in genomic sequence.\
</P>\
\
<P>Large recent duplications (&gt;= 1 kb and &gt;= 90% identity) were detected\
by identifying high-copy repeats, removing these repeats from the genomic \
sequence (&quot;fuguization&quot;) and searching all sequence for similarity. The\
repeats were then reinserted into the pairwise alignments, the ends of \
alignments trimmed, and global alignments were generated.\
For a full description of the &quot;fuguization&quot; detection method, see Bailey\
<em>et al.</em>, 2001. This method has become\
known as WGAC (whole-genome assembly comparison); for example, see Bailey \
<em>et al.</em>, 2002.\
\
<H2>Credits</H2>\
<P>\
These data were provided by Ginger Cheng, Xinwei She,\
<A HREF="mailto:&#97;r&#97;&#106;&#97;&#64;&#117;&#119;.ed&#117;">Archana Raja</A>,\
<A HREF="mailto:&#116;&#105;&#110;l&#111;&#117;&#105;&#101;&#64;&#117;.\
&#119;a&#115;&#104;&#105;&#110;&#103;&#116;&#111;&#110;.\
ed&#117;">Tin Louie</A> and\
<A HREF="mailto:&#101;&#101;e&#64;&#103;s.&#119;&#97;&#115;&#104;&#105;&#110;&#103;&#116;&#111;n.&#101;&#100;&#117;">Evan Eichler</A> \
at the <A HREF="http://eichlerlab.gs.washington.edu/" \
TARGET=_BLANK>University of Washington</A>. </P>\
\
<H2>References</H2>\
<P>\
Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, \
Myers EW, Li PW, Eichler EE.\
<A HREF="https://science.sciencemag.org/content/297/5583/1003"\
TARGET=_BLANK>Recent segmental duplications in the human genome</A>.\
<em>Science</em>. 2002 Aug 9;297(5583):1003-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12169732" target="_blank">12169732</a>\
</p>\
\
<P>\
Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE.\
<A HREF="https://genome.cshlp.org/content/11/6/1005.long"\
TARGET=_blank>Segmental duplications: organization and impact within the \
current human genome project assembly</A>.\
<em>Genome Res</em>. 2001 Jun;11(6):1005-17.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11381028" target="_blank">11381028</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311093/" target="_blank">PMC311093</a>\
</p>\
	varRep	1	group varRep\
longLabel Duplications of >1000 Bases of Non-RepeatMasked Sequence\
noScoreFilter .\
shortLabel Segmental Dups\
track genomicSuperDups\
type bed 6 +\
visibility hide\

wgEncodeLicrRnaSeqViewSignal	sgnal	bed 3	RNA-seq from ENCODE/LICR	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel RNA-seq from ENCODE/LICR\
maxHeightPixels 100:24:16\
parent wgEncodeLicrRnaSeq\
shortLabel sgnal\
track wgEncodeLicrRnaSeqViewSignal\
transformFunc NONE\
view Signal\
viewLimits 0:50\
visibility full\
windowingFunction mean+whiskers\

sgpGene	SGP Genes	genePred sgpPep	SGP Gene Predictions Using Mouse/Human Homology	0	100	0	90	100	127	172	177	0	0	0			<h2>Description</h2>\
\
This track shows gene predictions from the\
<a href="https://genome.crg.cat/services/sgp2/" target="_blank">SGP2</a>\
homology-based gene prediction program developed by Roderic Guig&oacute;'s\
&quot;<a href="https://www.crg.eu/roderic_guigo"\
target="_blank">Computational Biology of RNA Processing</a>&quot;\
group, which is part of the <a href="https://www.crg.eu/"\
target="_blank">Centre de Regulaci&oacute; Gen&ograve;mica</a>\
(CRG) in Barcelona, Catalunya, Spain. To predict\
genes in a genomic query, SGP2 combines geneid predictions with tblastx\
comparisons of the genome of the target species against genomic sequences\
of other species (reference genomes) deemed to be at an appropriate\
evolutionary distance from the target.\
\
<h2>Credits</h2>\
\
Thanks to the\
&quot;<a href="https://www.crg.eu/roderic_guigo"\
target="_blank">Computational Biology of RNA Processing</a>&quot;\
group for providing these data.\
	genes	1	color 0,90,100\
group genes\
longLabel SGP Gene Predictions Using Mouse/Human Homology\
shortLabel SGP Genes\
track sgpGene\
type genePred sgpPep\
visibility hide\

sibTxGraph	SIB Alt-Splicing	altGraphX	Alternative Splicing Graph from Swiss Institute of Bioinformatics	0	100	0	0	0	127	127	127	0	0	0		http://ccg.vital-it.ch/cgi-bin/tromer/tromergraph2draw.pl?db=mm9&species=M.+musculus&tromer=$$	<H2>Description</H2>\
<P>\
This track shows the graphs constructed by analyzing experimental RNA\
transcripts and serves as basis for the predicted alternative splicing\
transcripts shown in the SIB Genes track.  The blocks represent exons; lines\
indicate introns. The graphical display is drawn such that no exons\
overlap, making alternative events easier to view when the track is in full\
display mode and the resolution is set to approximately gene-level.  </P>\
<P>Further information on the graphs can be found on the\
<A HREF="https://ccg.vital-it.ch/tromer/" TARGET="_BLANK">Transcriptome \
Web interface</A>.</P>\
\
<H2>Methods</H2>\
<P>\
The splicing graphs were generated using a multi-step pipeline:  \
<OL>\
<LI>RefSeq and GenBank RNAs and ESTs are aligned to the genome with\
<A HREF="http://sibsim4.sourceforge.net" TARGET="_BLANK">SIBsim4</A>, keeping \
only the best alignments for each RNA.\
<LI>Alignments are broken up at non-intronic gaps, with small isolated \
fragments thrown out.\
<LI>A splicing graph is created for each set of overlapping alignments.  This\
graph has an edge for each exon or intron, and a vertex for each splice site,\
start, and end.  Each RNA that contributes to an edge is kept as evidence for\
that edge.\
<LI>Graphs consisting solely of unspliced ESTs are discarded.\
</OL></P>\
\
<H2>Credits</H2>\
<P>\
The SIB Alternative Splicing Graphs track was produced on the <A\
HREF="https://www.vital-it.ch/" TARGET="_BLANK">Vital-IT</A> high-performance \
computing platform\
using a computational pipeline developed by Christian Iseli with help from\
colleagues at the <A HREF="https://www.ludwigcancerresearch.org/" TARGET="_BLANK">Ludwig \
Institute for Cancer\
Research</A> and the <A HREF="https://www.sib.swiss/" TARGET="_BLANK">Swiss \
Institute of Bioinformatics</A>.  It is based on data from NCBI <A\
HREF="https://www.ncbi.nlm.nih.gov/refseq/" TARGET="_blank">RefSeq</A> and <A\
HREF="https://www.ncbi.nlm.nih.gov/genbank/"\
TARGET="_blank">GenBank</A>/<A HREF="https://www.embl.de" \
TARGET="_BLANK">EMBL</A>.  Our\
thanks to the people running these databases and to the scientists worldwide\
who have made contributions to them.</P>\
	rna	1	group rna\
idInUrlSql select name from sibTxGraph where id=%s\
longLabel Alternative Splicing Graph from Swiss Institute of Bioinformatics\
shortLabel SIB Alt-Splicing\
track sibTxGraph\
type altGraphX\
url http://ccg.vital-it.ch/cgi-bin/tromer/tromergraph2draw.pl?db=mm9&species=M.+musculus&tromer=$$\
urlLabel SIB link:\
visibility hide\

wgEncodePsuDnaseViewSignal	Signal	bed 3	DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel DNaseI Hypersensitivity by Digital DNaseI from ENCODE/PSU\
maxHeightPixels 100:50:16\
maxLimit 9016\
minLimit 0\
parent wgEncodePsuDnase\
shortLabel Signal\
track wgEncodePsuDnaseViewSignal\
view Signal\
viewLimits 0:0.15\
visibility full\
windowingFunction mean+whiskers\

wgEncodePsuHistoneViewSignal	Signal	bed 3	Histone Modifications by ChIP-seq from ENCODE/PSU	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
configurable on\
longLabel Histone Modifications by ChIP-seq from ENCODE/PSU\
maxHeightPixels 100:50:16\
parent wgEncodePsuHistone\
shortLabel Signal\
track wgEncodePsuHistoneViewSignal\
view Signal\
viewLimits 2:200\
visibility full\
windowingFunction mean+whiskers\

wgEncodeCaltechHistViewSignal	Signal	bed 3	Histone Modifications by ChIP-seq from ENCODE/Caltech	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel Histone Modifications by ChIP-seq from ENCODE/Caltech\
maxHeightPixels 100:32:0\
parent wgEncodeCaltechHist\
shortLabel Signal\
track wgEncodeCaltechHistViewSignal\
view Signal\
viewLimits 0:1\
visibility full\
windowingFunction mean+whiskers\

wgEncodeCaltechTfbsViewSignal	Signal	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/Caltech\
maxHeightPixels 100:32:0\
parent wgEncodeCaltechTfbs\
shortLabel Signal\
track wgEncodeCaltechTfbsViewSignal\
view Signal\
viewLimits 0:1\
visibility full\
windowingFunction mean+whiskers\

wgEncodeLicrHistoneViewSignal	Signal	bed 3	Histone Mods by ChIP-seq from ENCODE/LICR	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
configurable on\
longLabel Histone Mods by ChIP-seq from ENCODE/LICR\
maxHeightPixels 100:32:0\
parent wgEncodeLicrHistone\
shortLabel Signal\
track wgEncodeLicrHistoneViewSignal\
view Signal\
viewLimits 0.2:15\
visibility full\
windowingFunction mean+whiskers\

wgEncodeUwDnaseViewRawSignal	Signal	bed 3	DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington\
maxHeightPixels 100:32:16\
maxLimit 127303.00\
minLimit 1\
parent wgEncodeUwDnase\
shortLabel Signal\
track wgEncodeUwDnaseViewRawSignal\
view Signal\
viewLimits 1:100\
visibility full\
windowingFunction mean+whiskers\

wgEncodeLicrTfbsViewSignal	Signal	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
configurable on\
longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/LICR\
maxHeightPixels 100:32:0\
parent wgEncodeLicrTfbs\
shortLabel Signal\
track wgEncodeLicrTfbsViewSignal\
view Signal\
viewLimits 0.2:15\
visibility full\
windowingFunction mean+whiskers\

wgEncodeCaltechRnaSeqViewSignal	Signal	bed 3	RNA-seq from ENCODE/Caltech	0	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale on\
longLabel RNA-seq from ENCODE/Caltech\
maxHeightPixels 100:24:16\
parent wgEncodeCaltechRnaSeq\
shortLabel Signal\
track wgEncodeCaltechRnaSeqViewSignal\
transformFunc NONE\
view Signal\
viewLimits 0:500\
visibility hide\
windowingFunction mean+whiskers\

wgEncodeSydhHistViewSig	Signal	bed 3	Histone Modifications by ChIP-seq from ENCODE/SYDH	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel Histone Modifications by ChIP-seq from ENCODE/SYDH\
maxHeightPixels 100:16:16\
parent wgEncodeSydhHist\
shortLabel Signal\
track wgEncodeSydhHistViewSig\
view Signal\
viewLimits 10:20\
visibility full\
windowingFunction mean+whiskers\

polyASeqSitesSignalView	Signal	bigWig -1 2	Poly(A)-sequencing from Merck Research Laboratories	2	100	0	0	0	127	127	127	0	0	0				rna	0	autoScale on\
longLabel Poly(A)-sequencing from Merck Research Laboratories\
maxHeightPixels 50:50:5\
parent polyASeqSites\
shortLabel Signal\
track polyASeqSitesSignalView\
type bigWig -1 2\
view Signal\
visibility full\
yLineOnOff on\

wgEncodeUwRnaSeqViewMinusRawSig	Signal	bed 3	RNA-seq from ENCODE/UW	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel RNA-seq from ENCODE/UW\
maxHeightPixels 100:24:16\
parent wgEncodeUwRnaSeq\
shortLabel Signal\
track wgEncodeUwRnaSeqViewMinusRawSig\
transformFunc NONE\
view MinusRawSignal\
viewLimits 0:50\
visibility full\
windowingFunction mean+whiskers\

wgEncodeUwRnaSeqViewSignal	Signal	bed 3	RNA-seq from ENCODE/UW	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel RNA-seq from ENCODE/UW\
maxHeightPixels 100:24:16\
parent wgEncodeUwRnaSeq\
shortLabel Signal\
track wgEncodeUwRnaSeqViewSignal\
transformFunc NONE\
view Signal\
viewLimits 0:50\
visibility full\
windowingFunction mean+whiskers\

wgEncodeUwRnaSeqViewPlusRawSig	Signal	bed 3	RNA-seq from ENCODE/UW	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel RNA-seq from ENCODE/UW\
maxHeightPixels 100:24:16\
parent wgEncodeUwRnaSeq\
shortLabel Signal\
track wgEncodeUwRnaSeqViewPlusRawSig\
transformFunc NONE\
view PlusRawSignal\
viewLimits 0:50\
visibility full\
windowingFunction mean+whiskers\

wgEncodePsuTfbsViewSignal	Signal	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
configurable on\
longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/PSU\
maxHeightPixels 100:50:16\
parent wgEncodePsuTfbs\
shortLabel Signal\
track wgEncodePsuTfbsViewSignal\
view Signal\
viewLimits 5:100\
visibility full\
windowingFunction mean+whiskers\

wgEncodeUwDgfViewSignal	Signal	bed 3	DNaseI Digital Genomic Footprinting from ENCODE/University of Washington	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel DNaseI Digital Genomic Footprinting from ENCODE/University of Washington\
maxHeightPixels 100:32:16\
maxLimit 70530\
minLimit 1\
parent wgEncodeUwDgf\
shortLabel Signal\
track wgEncodeUwDgfViewSignal\
view Signal\
viewLimits 2:20\
visibility full\
windowingFunction mean+whiskers\

wgEncodePsuRnaSeqViewSignal	Signal	bed 3	RNA-seq from ENCODE/PSU	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel RNA-seq from ENCODE/PSU\
maxHeightPixels 100:50:16\
parent wgEncodePsuRnaSeq\
shortLabel Signal\
track wgEncodePsuRnaSeqViewSignal\
transformFunc NONE\
view Signal\
viewLimits 0:1000\
visibility full\
windowingFunction mean+whiskers\

simpleRepeat	Simple Repeats	bed 4 +	Simple Tandem Repeats by TRF	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>\
This track displays simple tandem repeats (possibly imperfect repeats) located\
by <A HREF="https://tandem.bu.edu/trf/trf.submit.options.html" \
TARGET=_blank>Tandem Repeats\
Finder</A> (TRF) which is specialized for this purpose. These repeats can\
occur within coding regions of genes and may be quite\
polymorphic. Repeat expansions are sometimes associated with specific\
diseases.</P>\
\
<H2>Methods</H2>\
<P>\
For more information about the TRF program, see Benson (1999).\
</P>\
\
<H2>Credits</H2>\
<P>\
TRF was written by \
<A HREF="https://tandem.bu.edu/benson.html" TARGET=_blank>Gary Benson</A>.</P>\
\
<H2>References</H2>\
\
<p>\
Benson G.\
<a href="https://academic.oup.com/nar/article/27/2/573/1061099/Tandem-repeats-finder-a-program-to-analyze-DNA" target="_blank">\
Tandem repeats finder: a program to analyze DNA sequences</a>.\
<em>Nucleic Acids Res</em>. 1999 Jan 15;27(2):573-80.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/9862982" target="_blank">9862982</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC148217/" target="_blank">PMC148217</a>\
</p>\
	varRep	1	group varRep\
longLabel Simple Tandem Repeats by TRF\
shortLabel Simple Repeats\
track simpleRepeat\
type bed 4 +\
visibility hide\

wgEncodeSydhTfbsViewSig	Snal	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale	2	100	0	0	0	127	127	127	0	0	0				regulation	1	autoScale off\
longLabel Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale\
maxHeightPixels 100:16:16\
parent wgEncodeSydhTfbs\
shortLabel Snal\
track wgEncodeSydhTfbsViewSig\
view Signal\
viewLimits 2:20\
visibility full\
windowingFunction mean+whiskers\

wgEncodeCshlLongRnaSeqViewJunctions	Splice Junctions	bed 3	Long RNA-seq from ENCODE/Cold Spring Harbor Lab	0	100	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Long RNA-seq from ENCODE/Cold Spring Harbor Lab\
parent wgEncodeCshlLongRnaSeq\
scoreFilter 0\
scoreFilterLimits 0:1000\
shortLabel Splice Junctions\
track wgEncodeCshlLongRnaSeqViewJunctions\
view Junctions\
visibility hide\

wgEncodeSydhHist	Stan/Yale Histone	bed 3	Histone Modifications by ChIP-seq from ENCODE/SYDH	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<P>This track shows probable locations of the specified histone modifications in\
the given cell types as determined by chromatin immunoprecipitation followed by \
high-throughput sequencing (ChIP-Seq). Each experiment is associated with an \
input signal which represents the control condition where immunoprecipitation \
with non-specific immunoglobulin was performed in the same cell type. For each \
experiment (cell type vs. antibody), this track shows a graph of enrichment for \
histone modification (<I>Signal</I>) along with sites that have the greatest \
evidence of histone modification, as identified by the PeakSeq algorithm (<I>Peaks</I>).\
<P>\
The sequence reads, quality scores, and alignment coordinates from\
these experiments are available for download.\
</P>\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
<DL>\
<DT><I>Peaks</I></DT><DD> Regions of signal enrichment based on processed data\
(normalized data from pooled replicates). ENCODE Peaks tables contain\
fields for statistical significance, including FDR\
(<a href="/goldenPath/help/qValue.html" target="_blank">qValue</a>).</DD>\
<DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based on\
processed data.</DD>\
</DL>\
\
<H2>Methods</H2>\
\
<P>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
For details on the chromatin immunoprecipitation protocol used, \
see Euskirchen <EM>et al.</EM> (2007), Rozowsky <EM>et al.</EM> (2009) \
and Auerbach <EM>et al.</EM> (2009).\
</P>\
<P>\
DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa)\
sequencing platform and mapped to the genome using the Eland alignment program.\
ChIP-seq data was scored based on sequence reads (length ~30 bp) that align uniquely\
to the human genome. From the mapped tags, a signal map of ChIP DNA fragments\
(average fragment length ~200 bp) was constructed where the signal height was the number of\
overlapping fragments at each nucleotide position in the genome.\
</P>\
<P>\
For each 1 Mb segment of each chromosome, a peak height threshold was determined\
 by requiring a false discovery rate &lt;= 0.01 when comparing the number of peaks\
 above said threshold to the number of peaks obtained from multiple simulations of a\
 random null background with the same number of mapped reads (also accounting \
for the fraction of mapable bases for sequence tags in that 1 Mb segment). The\
 number of mapped tags in a putative binding region was compared to the normalized\
 (normalized by correlating tag counts in genomic 10 kb windows) number of \
mapped tags in the same region from an input DNA control. Using a binomial test,\
 only regions that had a p-value &lt;= 0.01 were considered to be significantly \
enriched compared to the input DNA control.\
</P>\
\
<h2>Release Notes</h2>\
\
<p>\
This is Release 2 (August 2012). It contains a total of 12 new experiments on\
histone modifications including 1 new cell line and 5 new antibodies.\
</p>\
\
<H2>Errata</H2>\
<P>\
At the request of the data provider, data files and table related to\
experiment wgEncodeEM003324 (H3K27ac in MEL cells) have been removed.\
An incorrect antibody was used in this experiment.\
</P>\
\
<H2>Credits</H2>\
\
<P>These data were generated and analyzed by the labs of\
<A HREF="https://med.stanford.edu/snyderlab.html"\
  class="external text" title="https://med.stanford.edu/snyderlab.html"\
  target="_blank">Michael Snyder</a> at Stanford University and\
<A HREF="https://medicine.yale.edu/genetics/people/sherman_weissman.profile"\
  class="external text" title="https://medicine.yale.edu/genetics/people/sherman_weissman.profile"\
  target="_blank">Sherman Weissman</a> at Yale University.\
&nbsp;&nbsp;\
</p>\
<p>\
Contact: <A \
HREF="mailto:&#112;c&#97;&#121;&#116;&#105;n&#103;&#64;&#115;&#116;&#97;n&#102;\
o&#114;&#100;.&#101;d&#117;"\
 title="mailto:&#112;c&#97;&#121;&#116;&#105;n&#103;&#64;&#115;&#116;&#97;n&#102;\
o&#114;&#100;.&#101;d&#117;" rel="nofollow"\
  TARGET=_BLANK>Philip Cayting</A>\
<!-- above address is (Philip Cayting) pcayting at stanford.edu -->\
</P>\
<!-- #SYDH -->\
\
<H2>References</H2>\
\
<p>\
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefran&#231;ois P, Struhl K, Gerstein M, Snyder M.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19706456" target="_blank">\
Mapping accessible chromatin regions using Sono-Seq</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2009 Sep 1;106(35):14926-31.\
</p>\
\
<p>\
Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17568005" target="_blank">\
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies</a>.\
<em>Genome Res</em>. 2007 Jun;17(6):898-909.\
</p>\
\
<p>\
Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/14527995" target="_blank">\
Distribution of NF-kappaB-binding sites across human chromosome 22</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Oct 14;100(21):12247-52.\
</p>\
\
<p>\
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17558387" target="_blank">\
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing</a>.\
<em>Nat Methods</em>. 2007 Aug;4(8):651-7.\
</p>\
\
<p>\
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19122651" target="_blank">\
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls</a>.\
<em>Nat Biotechnol</em>. 2009 Jan;27(1):66-75.\
</p>\
\
<H2>Data Release Policy</H2>\
\
Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
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wgEncodeSydhRnaSeq	Stan/Yale RNA-seq	bed 3	RNA-seq from ENCODE/Stanford/Yale	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<P>\
This track shows enrichment of RNA sequence tags mapped to the mouse genome generated by high \
throughput sequencing (RNA-Seq).  Double stranded cDNA was synthesized from enriched RNA\
that was obtained after depletion of ribosomal RNA.  Pieces of cDNA, 300-350 nucleotides \
in length, were PCR amplified, adapter ligated, and sequenced on an Illumina HiSeq sequencer.\
</p>\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>\
The Alignments view shows reads mapped to the genome and indicates where\
bases may mismatch.  The alignment file follows the standard SAM format of Bowtie output.  See the <a href="http://bowtie-bio.sourceforge.net/manual.shtml#sam-bowtie-output" target=_blank>Bowtie Manual</a> for more information about the SAM Bowtie output and the <a href="http://samtools.github.io/hts-specs/SAMv1.pdf#page=4" target=_blank>SAM Format Specification</a> for more information on the SAM/BAM file format. \
</P>\
\
<H2>Methods</H2>\
\
<P>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell" target="_blank">ENCODE cell culture protocols</a>.\
\
Total RNA was extracted using RNeasy Mini Kit (74104, Aiagen), following the manufacturer's protocol.  Ribosomal RNA was removed from total RNA using the Ribo-Zero Gold Kits (MRZG126, Epicentre).  Double-stranded cDNA synthesis was performed on the rRNA depleted RNA using random primers and the SuperScript double-stranded cDNA synthesis kit (11917-010, Life Tech).  After first strand cDNA synthesis, NucAway Spin Column (Ambion cat. 100070-30) was used to remove dNTPs.  In the second strand cDNA synthesis reaction, dTTP in the dNTP mix was substituted with dUTP.  After end repair and addition of 'A' base to 3' end, illumina paired-end adapter was ligated to Double-stranded cDNA library.  After gel size selection of adapter ligated cDNA (300-350), Uracil-N-Glycosylase (UNG: Applied Biosystems) was used to digest the second strand cDNA (Parkhomchuk <EM>et al. </EM>, 2009).  PCR amplified adapter ligated cDNA was sequenced using Illumina HiSeq.  Sequence reads of 2x101 nt long with 0-2 mismatches were mapped to the mouse genome (version mm9) using the BWA aligner, version 0.5.7.  The signal height corresponds to the number of overlapping fragments at each nucleotide position in the genome.\
</P>\
\
<H2>Release Notes</H2>\
\
<P>\
This is Release 2 (August 12) of this track. The bigwig file for the MEL cell, replicate 2 with no treatment, was corrupt and has been replaced.  \
</P>\
\
<H2>Credits</H2>\
\
<P>These data were generated and analyzed by the labs of\
<A HREF="https://med.stanford.edu/snyderlab.html"\
  class="external text" title="https://med.stanford.edu/snyderlab.html"\
  target="_blank">Michael Snyder</a>.\
<P>\
&nbsp;Contact: <A \
HREF="mailto:&#112;c&#97;&#121;&#116;&#105;n&#103;&#64;&#115;&#116;&#97;n&#102;\
o&#114;&#100;.&#101;d&#117;"\
 title="mailto:&#112;c&#97;&#121;&#116;&#105;n&#103;&#64;&#115;&#116;&#97;n&#102;\
 o&#114;&#100;.&#101;d&#117;" rel="nofollow" TARGET=_BLANK>Philip Cayting</A>.\
 <!-- above address is (Philip Cayting) pcayting at stanford.edu -->\
</P>\
\
<H2>References</H2>\
\
<p>\
Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A.\
<a href="https://academic.oup.com/nar/article/37/18/e123/1085684" target="_blank">\
Transcriptome analysis by strand-specific sequencing of complementary DNA</a>.\
<em>Nucleic Acids Res</em>. 2009 Oct;37(18):e123.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19620212" target="_blank">19620212</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764448/" target="_blank">PMC2764448</a>\
</p>\
\
<H2>Data Release Policy</H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column on the track configuration page and\
the download page.  The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
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html wgEncodeSydhRnaSeq.release2\
longLabel RNA-seq from ENCODE/Stanford/Yale\
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wgEncodeSydhTfbs	Stan/Yale TFBS	bed 3	Transcription Factor Binding Sites by ChIP-seq from ENCODE/Stanford/Yale	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<P>This track shows probable binding sites of the specified transcription \
factors (TFs) in the given cell types as determined by chromatin \
immunoprecipitation followed by high throughput sequencing (ChIP-seq). \
Each experiment is associated with an input signal, which represents the \
control condition where immunoprecipitation with non-specific immunoglobulin \
was performed in the same cell type. For each experiment (cell type vs. \
antibody) this track shows a graph of enrichment for TF binding (<I>Signal</I>),\
along with sites that have the greatest evidence of transcription factor \
binding, as identified by the PeakSeq algorithm (<I>Peaks</I>).\
<P>\
The sequence reads, quality scores, and alignment coordinates from\
these experiments are available for download.\
</P>\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>).  For each view, there are multiple subtracks that\
display individually on the browser.  Instructions for configuring multi-view\
tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
<DL>\
<DT><I>Peaks</I></DT><DD> Regions of signal enrichment based on processed data\
(normalized data from pooled replicates). Intensity is represented in \
grayscale, the darker shading shows higher intensity (a solid vertical line\
in the peak region represents the the point with the highest signal).\
ENCODE Peaks tables contain fields for statistical significance, \
including the minimum false discovery rate (FDR) threshold at which the test may be called significant\
(<a href="/goldenPath/help/qValue.html" target="_blank">qValue</a>).</DD>\
<DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based on\
processed data.</DD>\
</DL>\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
\
<H2>Methods</H2>\
\
<P>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
For details on the chromatin immunoprecipitation protocol used, \
see (Euskirchen <EM>et al.</EM>, 2007), (Rozowsky <EM>et al.</EM>, 2009) \
and (Auerbach <EM>et al.</EM>, 2009).\
</P>\
<P>\
DNA recovered from the precipitated chromatin was sequenced on the Illumina (Solexa)\
sequencing platform and mapped to the genome using the Eland alignment program.\
ChIP-seq data was scored based on sequence reads (length ~30 bps) that align uniquely\
to the human genome. From the mapped tags, a signal map of ChIP DNA fragments\
(average fragment length ~ 200 bp) was constructed where the signal height is the number of\
overlapping fragments at each nucleotide position in the genome. Reads were pooled from \
all submitted replicates to generate the Peak and Signal files. Per-replicate\
aligments and sequences are available for download at\
<A HREF="http://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/"\
 TARGET=_BLANK>downloads page</A>.\
</P>\
<P>\
For each 1 Mb segment of each chromosome, a peak height threshold was determined\
by requiring a false discovery rate &lt;= 0.01 when comparing the number of peaks\
above said threshold to the number of peaks obtained from multiple simulations of a\
random null background with the same number of mapped reads (also accounting\
for the fraction of mapable bases for sequence tags in that 1 Mb segment). The\
number of mapped tags in a putative binding region is compared to the normalized\
(normalized by correlating tag counts in genomic 10 kb windows) number of \
mapped tags in the same region from an input DNA control. Using a binomial test,\
only regions that have a p-value &le; 0.01 are considered to be significantly \
enriched compared to the input DNA control.\
</P>\
\
<h2>Release Notes</h2>\
\
<P>\
This is Release 4 (August 2012). It contains a total of 88 ChIP-seq experiments on transcriptions factor binding with the addition of 22 new \
experiments including 12 new antibodies. \
</P>\
<P>\
Previous versions of files are available for download from the\
<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeSydhTfbs/"\
TARGET=_BLANK>FTP site</A>.\
</P>\
\
<H2>Credits</H2>\
\
<P>These data were generated and analyzed by the labs of\
<A HREF="https://med.stanford.edu/snyderlab.html"\
  class="external text" title="https://med.stanford.edu/snyderlab.html"\
  target="_blank">Michael Snyder</a> at Stanford University and\
<A HREF="https://medicine.yale.edu/genetics/people/sherman_weissman.profile"\
  class="external text" title="https://medicine.yale.edu/genetics/people/sherman_weissman.profile"\
  target="_blank">Sherman Weissman</a> at Yale University.\
</P>\
<P>\
Contact: <A \
HREF="mailto:&#112;c&#97;&#121;&#116;&#105;n&#103;&#64;&#115;&#116;&#97;n&#102;\
o&#114;&#100;.&#101;d&#117;"\
 title="mailto:&#112;c&#97;&#121;&#116;&#105;n&#103;&#64;&#115;&#116;&#97;n&#102;\
o&#114;&#100;.&#101;d&#117;" rel="nofollow"\
  TARGET=_BLANK>Philip Cayting</A>.\
<!-- above address is (Philip Cayting) pcayting at stanford.edu -->\
</P>\
\
<H2>References</H2>\
\
<p>\
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefran&#231;ois P, Struhl K, Gerstein M, Snyder M.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19706456" target="_blank">\
Mapping accessible chromatin regions using Sono-Seq</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2009 Sep 1;106(35):14926-31.\
</p>\
\
<p>\
Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17568005" target="_blank">\
Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies</a>.\
<em>Genome Res</em>. 2007 Jun;17(6):898-909.\
</p>\
\
<p>\
Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/14527995" target="_blank">\
Distribution of NF-kappaB-binding sites across human chromosome 22</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Oct 14;100(21):12247-52.\
</p>\
\
<p>\
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/17558387" target="_blank">\
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing</a>.\
<em>Nat Methods</em>. 2007 Aug;4(8):651-7.\
</p>\
\
<p>\
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/19122651" target="_blank">\
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls</a>.\
<em>Nat Biotechnol</em>. 2009 Jan;27(1):66-75.\
</p>\
\
<H2>Data Release Policy</H2>\
\
<P>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column on the track configuration page and\
the download page.  The full data release policy for ENCODE is available\
<A HREF="../ENCODE/terms.html" TARGET=_BLANK>here</A>.</P>\
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subGroup1 view Views Peaks=Peaks Signal=Signal\
subGroup2 cellType Cell_Line CH12=CH12 ESE14=ES-E14 MEL=MEL\
subGroup3 factor Factor BHLHE40c=BHLHE40_(NB100-1800) CHD1NB10060411=CHD1_(NB100-60411) CHD2AB68301=CHD2 cJUN=c-Jun cMYBSC7874=c-Myb cMYC=c-Myc CORESTSC30189=COREST_(sc-30189) CTCFb=CTCF E2F4=E2F4 ETS1=ETS1 GATA1SC265=GATA-1 GCN5=GCN5 HCFC1NB10068209=HCFC1_(NB100-68209) JUND=JunD MAFKAB50322=MafK MAX=Max MAZAB85725=MAZ_(ab85725) MXI1AF4185=Mxi1 NELFE=NELFe NRF2=Nrf2 P300=p300 P300SC584=p300_(SC-584) POL2=Pol2 POL2S2=Pol2(phosphoS2) RAD21=Rad21 SIN3ANB6001263=SIN3A_(NB600-1263) SMC3ab9263=SMC3 TBP=TBP UBFSC13125=UBF&#95;(SC-13125) USF2=USF2 ZC3H11ANB10074650=ZC3H11A_(NB100-74650) ZKSCAN1HPA006672=ZKSCAN1&#95;(HPA006672) ZNF384HPA004051=ZNF384_(HPA004051) ZNFMIZDCP1AB65767=ZNF-MIZD-CP1_(ab65767) ZZZInputIGGMUS=Input_(<i>IgG-mus</i>) ZZZInputIGGRAB=Input_(<i>IgG-rab</i>) ZZZInputIGGRAT=Input_(<i>IgG-rat</i>) ZZZInputstd=Input_(<i>Standard</i>) ZZZInputIGGYALE=Input_(<i>IgG-Yale</i>)\
subGroup4 control Control IGGMUS=IgG-mus IGGRAB=IgG-rab IGGRAT=IgG-rat IGGYALE=IgG-Yale STD=std\
subGroup5 treatment Treatment zNONE=None DM2P5D=DMSO_2.0pct\
track wgEncodeSydhTfbs\
type bed 3\

transcriptome	Transcriptome	genePred	TROMER Transcriptome database	0	100	56	108	56	155	181	155	0	0	0		http://ccg.vital-it.ch/cgi-bin/tromer/tromer_quick_search.pl?db=mm9&query_str=$$	<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">\
<HTML>\
<HEAD>\
\	<META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">\
\	<TITLE></TITLE>\
\	<META NAME="GENERATOR" CONTENT="OpenOffice.org 2.3  (Linux)">\
\	<META NAME="CREATED" CONTENT="0;0">\
\	<META NAME="CHANGED" CONTENT="20080505;18391700">\
</HEAD>\
<BODY LANG="en-US" DIR="LTR">\
<H2>Description</H2>\
<P>The transcriptome track shows gene predictions based on data from\
RefSeq and EMBL/GenBank. This is a moderately conservative set of\
predictions, requiring the support of either one GenBank full length\
RNA sequence, one RefSeq RNA, or one spliced EST. The track includes\
both protein-coding and non-coding transcripts. The CDS are predicted\
using <A HREF="http://estscan.sourceforge.net/" target="_blank">ESTScan</A>.</P>\
<H2>Display Conventions and Configuration</H2>\
<P>This track in general follows the display conventions for\
<A HREF="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene\
prediction tracks</A>. The exons for putative noncoding genes and\
untranslated regions are represented by relatively thin blocks, while\
those for coding open reading frames are thicker.</P>\
<P>This track contains an optional codon coloring feature that allows\
users to quickly validate and compare gene predictions. To display\
codon colors, select the <EM>genomic codons</EM> option from the\
<EM>Color track by codons</EM> pull-down menu. Click\
<A HREF="../goldenPath/help/hgCodonColoring.html">here</A>\
for more information about this feature. \
</P>\
<P>Further information on the predicted transcripts can be found on\
the <A HREF="https://ccg.vital-it.ch/tromer/" target="_blank">Transcriptome Web\
interface</A>.</P>\
<H2>Methods</H2>\
<P>The transcriptome is built using a multi-step pipeline: \
</P>\
<OL>\
\	<LI><P STYLE="margin-bottom: 0in">RefSeq and GenBank RNAs and ESTs\
\	are aligned to the genome with <A HREF="http://sibsim4.sourceforge.net/"\
        target="_blank">SIBsim4</A>,\
\	keeping only the best alignments for each RNA. \
\	</P>\
\	<LI><P STYLE="margin-bottom: 0in">Alignments are broken up at\
\	non-intronic gaps, with small isolated fragments thrown out. \
\	</P>\
\	<LI><P STYLE="margin-bottom: 0in">A splicing graph is created for\
\	each set of overlapping alignments. This graph has an edge for each\
\	exon or intron, and a vertex for each splice site, start, and end.\
\	Each RNA that contributes to an edge is kept as evidence for that\
\	edge. \
\	</P>\
\	<LI><P STYLE="margin-bottom: 0in">The graph is traversed to generate\
\	all unique transcripts. The traversal is guided by the initial RNAs\
\	to avoid a combinatorial explosion in alternative splicing. \
\	</P>\
\	<LI><P>Protein predictions are generated. \
\	</P>\
</OL>\
<H2>Credits</H2>\
<P>The transcriptome track was produced on the <A HREF="https://www.vital-it.ch/"\
target="_blank">Vital-IT</A> high-performance computing platform using a computational pipeline\
developed by Christian Iseli with help from colleagues at the\
<A HREF="https://www.ludwigcancerresearch.org/" target="_blank">Ludwig institute for Cancer\
Research</A> and the <A HREF="https://www.sib.swiss/" target="_blank">Swiss\
Institute of Bioinformatics</A>. It is based on data from NCBI\
<A HREF="https://www.ncbi.nlm.nih.gov/refseq/" TARGET="_blank">RefSeq</A>\
and <A HREF="https://www.ncbi.nlm.nih.gov/genbank/" TARGET="_blank">GenBank</A>/\
<A HREF="https://www.embl.org/" target="_blank">EMBL</A>.\
Our thanks to the people running these databases and to the\
scientists worldwide who have made contributions to them. \
</P>\
<H2>References</H2>\
<p>\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
<a href="https://academic.oup.com/nar/article/32/suppl_1/D23/2505202" target="_blank">\
GenBank: update</a>.\
<em>Nucleic Acids Res</em>. 2004 Jan 1;32(Database issue):D23-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14681350" target="_blank">14681350</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308779/" target="_blank">PMC308779</a>\
</p>\
</BODY>\
</HTML>\
	genes	1	color 56,108,56\
group genes\
longLabel TROMER Transcriptome database\
shortLabel Transcriptome\
track transcriptome\
type genePred\
url http://ccg.vital-it.ch/cgi-bin/tromer/tromer_quick_search.pl?db=mm9&query_str=$$\
urlLabel TROMER database detail:\

tRNAs	tRNA Genes	bed 6 +	Transfer RNA Genes Identified with tRNAscan-SE	0	100	0	20	150	127	137	202	0	0	0			<H2>Description</H2>\
<P>\
This track displays tRNA genes predicted by using \
<A HREF="http://lowelab.ucsc.edu/tRNAscan-SE/" TARGET=_blank>tRNAscan-SE</A> v.1.23. \
</P>\
<P>\
tRNAscan-SE is an integrated program that uses tRNAscan (Fichant) and an A/B box motif detection \
algorithm (Pavesi) as pre-filters to obtain an initial list of tRNA candidates. \
The program then filters these candidates with a covariance model-based \
search program <A HREF="http://eddylab.org/software.html" TARGET=_blank>\
COVE</A> (Eddy) to obtain a highly specific set of primary sequence \
and secondary structure predictions that represent 99-100% of true tRNAs \
with a false positive rate of fewer than 1 per 15 gigabases.</P>\
<P>\
Detailed tRNA annotations for eukaryotes, bacteria, and archaea are available at\
<A HREF="http://gtrnadb.ucsc.edu" TARGET=_blank>Genomic tRNA Database (GtRNAdb)</A>. \
</P>\
<P>\
What does the tRNAscan-SE score mean?  Anything with a score above 20 bits is likely to be\
<I>derived</I> from a tRNA, although this does not indicate whether the tRNA gene still encodes a \
functional tRNA molecule (i.e. tRNA-derived SINES probably do not function in the ribosome in translation).\
Vertebrate tRNAs with scores of &gt;60.0 (bits) are likely to encode functional tRNA genes, and \
those with scores below ~45 have sequence or structural features that indicate they probably are\
no longer involved in translation.  tRNAs with scores between 45-60 bits are in the &quot;grey&quot; zone, and may\
or may not have all the required features to be functional.  In these cases, tRNAs should be inspected\
carefully for loss of specific primary or secondary structure features (usually in alignments with other\
genes of the same isotype), in order to make a better educated guess.  These rough score range guides \
are not exact, nor are they based on specific biochemical studies of atypical tRNA features,\
so please treat them accordingly.\
</P>\
<P>\
Please note that tRNA genes marked as &quot;Pseudo&quot; are low scoring predictions that are mostly pseudogenes or \
tRNA-derived elements. These genes do not usually fold into a typical cloverleaf tRNA secondary \
structure and the provided images of the predicted secondary structures may appear rotated.\
</P>\
\
<H2>Credits</H2>\
<P>\
Both tRNAscan-SE and GtRNAdb are maintained by the\
<A HREF="http://lowelab.ucsc.edu" TARGET=_blank>Lowe Lab</A> at UCSC.\
</P>\
<P>\
Cove-predicted tRNA secondary structures were rendered by NAVIEW (c) 1988 Robert E. Bruccoleri.\
</P>\
\
<H2>References</H2>\
<P>\
When making use of these data, please cite the following articles:</P>\
<P>\
Chan PP, Lowe TM. \
<A HREF="https://academic.oup.com/nar/article/37/suppl_1/D93/1010599/GtRNAdb-a-database-of-transfer-RNA-genes-detected" \
target="_blank">GtRNAdb: a database of transfer RNA genes detected in genomic sequence</a>.\
<em>Nucleic Acids Res</em>. 2009 Jan;37(Database issue):D93-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18984615" target="_blank">18984615</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686519/" target="_blank">PMC2686519</a>\
</p>\
\
<P>\
Eddy SR, Durbin R. \
<A HREF="https://academic.oup.com/nar/article/22/11/2079/2400118/RNA-sequence-analysis-using-covariance-models" TARGET=_blank>\
RNA sequence analysis using covariance models</a>.\
<em>Nucleic Acids Res</em>. 1994 Jun 11;22(11):2079-88.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8029015" target="_blank">8029015</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308124/" target="_blank">PMC308124</a>\
</p>\
\
<P>\
Fichant GA, Burks C. \
<A HREF="https://www.sciencedirect.com/science/article/pii/002228369190108I" TARGET=_blank>\
Identifying potential tRNA genes in genomic DNA sequences</a>.\
<em>J Mol Biol</em>. 1991 Aug 5;220(3):659-71.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/1870126" target="_blank">1870126</a>\
</P>\
\
<P>\
Lowe TM, Eddy SR. \
<A HREF="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/pdf/250955.pdf" TARGET=_blank>\
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence</a>.\
<em>Nucleic Acids Res</em>. 1997 Mar 1;25(5):955-64.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/9023104" target="_blank">9023104</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/" target="_blank">PMC146525</a>\
</P>\
\
<P>\
Pavesi A, Conterio F, Bolchi A, Dieci G, Ottonello S.\
<A HREF="https://academic.oup.com/nar/article/22/7/1247/1206900/Identification-of-new-eukaryotic-tRNA-genes-in" TARGET=_blank>\
Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix\
analysis of transcriptional control regions</a>.\
<em>Nucleic Acids Res</em>. 1994 Apr 11;22(7):1247-56.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/8165140" target="_blank">8165140</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC523650/" target="_blank">PMC523650</a>\
</p>\
	genes	1	color 0,20,150\
group genes\
longLabel Transfer RNA Genes Identified with tRNAscan-SE\
nextItemButton on\
noScoreFilter .\
shortLabel tRNA Genes\
track tRNAs\
type bed 6 +\
visibility hide\

targetScanS	TS miRNA sites	bed 6 .	TargetScan miRNA Regulatory Sites	0	100	0	96	0	127	175	127	0	0	0		http://www.targetscan.org/cgi-bin/targetscan/mmu_50/view_gene.cgi?gs=$P&taxid=10090&members=$p&showcnc=1	<H2>Description</H2>\
<P>\
This track shows conserved mammalian microRNA regulatory target sites\
for conserved microRNA families in\
the 3' UTR regions of Refseq Genes, as predicted by TargetScanMouse 5.1. </P> \
\
<H2>Method</H2>\
<P>\
Putative miRNA binding sites in UTRs were identified using seven-nucleotide\
seed regions from all known miRNA families conserved across mammals.\
Using all mouse RefSeq transcripts and CDS annotation from NCBI,\
aligned vertebrate 3' UTRs were extracted from multiz alignments and masked\
for overlap with protein-coding sequences.\
These 3' UTRs were scanned to identify conserved matches to the miRNA seed\
region, as in Friedman <EM>et al</EM>. (2009).\
These sites were then assigned a percentile rank (0 to 100) based on their\
context score (Grimson <EM>et al</EM>., 2007).\
For further details of the methods used to generate\
this annotation, see the references\
and the <A HREF="http://www.targetscan.org/" TARGET="_blank">TargetScan</A>\
website.</P>\
\
<H2>Credit</H2>\
<P>\
Thanks to George Bell of\
<A HREF="http://barc.wi.mit.edu/"\
TARGET="_blank">Bioinformatics and Research Computing</A> at the Whitehead\
Institute for providing this annotation, which was generated in collaboration\
with the labs of David Bartel and Chris Burge.\
Additional information on microRNA target prediction is available on the\
<A HREF="http://www.targetscan.org/" TARGET="_blank">TargetScan</A> website.\
</P>\
\
<H2>References</H2>\
<p>\
Friedman RC, Farh KK, Burge CB, Bartel DP.\
<a href="https://genome.cshlp.org/content/19/1/92.long" target="_blank">\
Most mammalian mRNAs are conserved targets of microRNAs</a>.\
<em>Genome Res</em>. 2009 Jan;19(1):92-105.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18955434" target="_blank">18955434</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2612969/" target="_blank">PMC2612969</a>\
</p>\
\
<p>\
Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP.\
<a href="https://www.sciencedirect.com/science/article/pii/S1097276507004078" target="_blank">\
MicroRNA targeting specificity in mammals: determinants beyond seed pairing</a>.\
<em>Mol Cell</em>. 2007 Jul 6;27(1):91-105.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17612493" target="_blank">17612493</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3800283/" target="_blank">PMC3800283</a>\
</p>\
\
<p>\
Lewis BP, Burge CB, Bartel DP.\
<a href="https://www.sciencedirect.com/science/article/pii/S0092867404012607" target="_blank">\
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are\
microRNA targets</a>.\
<em>Cell</em>. 2005 Jan 14;120(1):15-20.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15652477" target="_blank">15652477</a>\
</p>\
	regulation	1	color 0,96,0\
group regulation\
longLabel TargetScan miRNA Regulatory Sites\
priority 0\
scoreFilterMax 100\
shortLabel TS miRNA sites\
track targetScanS\
type bed 6 .\
url http://www.targetscan.org/cgi-bin/targetscan/mmu_50/view_gene.cgi?gs=$P&taxid=10090&members=$p&showcnc=1\
urlLabel TargetScan link:\
visibility hide\

knownAlt	UCSC Alt Events	bed 6 .	Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes	0	100	90	0	150	172	127	202	0	0	0			<H2>Description</H2>\
<P>This track shows various types of alternative splicing and other\
events that result in more than a single transcript from the same\
gene. The label by an item describes the type of event. The events are:</P>\
<UL>\
<LI>Alternate Promoter (<B>altPromoter</B>) - Transcription starts at multiple places.  The altPromoter extends from 100 bases before to 50 bases after transcription start.\
<LI>Alternate Finish Site (<B>altFinish</B>) - Transcription ends at multiple places.\
<LI>Cassette Exon (<B>cassetteExon</B>) - Exon is present in some transcripts but \
not others. These are found by looking for exons that overlap an intron in the \
same transcript.\
<LI>Retained Intron (<B>retainedIntron</B>) - Introns are spliced out in some \
transcripts but not others. In some cases, particularly when the intron is near \
the 3' end, this can reflect an incompletely processed transcript rather than \
a true alt-splicing event.\
<LI>Overlapping Exon (<B>bleedingExon</B>) - Initial or terminal exons overlap \
in an intron in another transcript. These often are associated with incompletely \
processed transcripts.\
<LI>Alternate 3' End (<B>altThreePrime</B>) - Variations on the 3' end of an intron.\
<LI>Alternate 5' End (<B>altFivePrime</B>) - Variations on the 5' end of an intron.\
<LI>Intron Ends have AT/AC (<B>atacIntron</B>) - An intron with AT/AC ends rather than \
the usual GT/AG. These are associated with the minor spliceosome.\
<LI>Strange Intron Ends (<B>strangeSplice</B>) - An intron with ends that are not \
GT/AG, GC/AG, or AT/AC. These are usually artifacts of some sort due to \
sequencing error or polymorphism.\
</UL>\
\
<H2>Credits</H2>\
<P>This track is based on an analysis by the <TT>txgAnalyse</TT> program of splicing graphs\
produced by the <TT>txGraph</TT> program. Both of these programs were written by Jim\
Kent at UCSC.</P>\
	genes	1	color 90,0,150\
group genes\
longLabel Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes\
noScoreFilter .\
shortLabel UCSC Alt Events\
track knownAlt\
type bed 6 .\
visibility hide\

wgEncodeUwDgf	UW DNaseI DGF	bed 3	DNaseI Digital Genomic Footprinting from ENCODE/University of Washington	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
\
<p>This track, produced as part of the mouse ENCODE Project, contains deep sequencing DNase data\
that will be used to identify sites where regulatory factors bind to the genome\
(<i>footprints</i>).</p>\
<p>Footprinting is a technique used to define the DNA sequences that interact\
with and bind DNA-binding proteins, such as transcription factors,\
zinc-finger proteins, hormone-receptor complexes, and other \
chromatin-modulating factors like CTCF.  The technique depends upon the\
strength and tight nature of protein-DNA interactions. In their native chromatin\
state, DNA sequences that interact directly with DNA-binding proteins are\
relatively protected from DNA degrading endonucleases, while the exposed/unbound\
portions are readily degraded by such endonucleases. A massively parallel\
next-generation sequencing technique to define the DNase hypersensitive sites\
in the genome was adopted. The DNase samples were sequenced using next-generation\
sequencing machines to significantly higher depths of 300-fold or greater. This produces\
a base-pair level resolution of the DNase susceptibility maps of the native\
chromatin state.  These base-pair resolution maps represent and are dependent\
upon the nature and the specificity of interaction of the DNA with the\
regulatory/modulatory proteins binding at specific loci in the genome; thus\
they represent the native chromatin state of the genome under investigation.\
The deep sequencing approach has been used to define the footprint landscape of\
the genome by identifying DNA motifs that interact with known or novel DNA\
binding proteins.\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track is a multi-view composite track that contains multiple data types\
(<EM>views</EM>). For each view, there are multiple subtracks that display\
individually on the browser. Instructions for configuring multi-view tracks\
are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
</p>\
For each cell type, this track contains the following views:\
<DL>\
<DT><I>HotSpots</I>\
<DD> DNaseI hypersensitive zones identified using the HotSpot algorithm.\
<DT><I>Peaks</I>\
<DD> DNaseI hypersensitive sites (DHSs) identified as signal peaks within \
FDR 1.0% hypersensitive zones.\
</DT>\
<DT><I>Signal</I>\
<DD>Per-base count of sequence reads whose 5' end (corresponding to a \
DNaseI-induced DNA cut) coincides with the given position.\
</DT>\
<DT><I>Raw Signal</I>\
<DD>The density of tags mapping within a 150 bp sliding window\
(at a 20 bp step across the genome).\
</DL>\
NOTE: The names of the signal views in this track are reversed from conventions used in\
other ENCODE tracks, where the less processed signal is termed "Raw".\
<p>DNaseI sensitivity is shown as the absolute density of <EM>in vivo</EM> \
cleavage sites across the genome mapped using the Digital DNaseI methodology \
(see below).  \
</p>\
\
<p>Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.</p>\
\
<h2>Methods</h2> \
\
<p>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture\
protocols</a>.  Digital DNaseI was performed by DNaseI digestion of\
intact nuclei, followed by isolating DNaseI "double-hit" fragments (Sabo <EM>et al.</EM>, 2006),\
and direct sequencing of fragment ends (which correspond to <EM>in vivo</EM> DNaseI cleavage\
sites) using the Solexa platform (27 bp reads).  High-quality reads were\
mapped to the NCBI37/mm9 mouse genome using Bowtie 0.12.5;\
only unique mappings were kept. DNaseI sensitivity is directly reflected \
in raw tag density (<I>Raw Signal</I>), which is shown\
in the track as density of tags mapping within a 150 bp sliding window\
(at a 20 bp step across the genome).  DNaseI hypersensitive zones\
(<I>HotSpots</I>) were identified using the HotSpot algorithm (Sabo <EM>et al.</EM>, 2004).\
False discovery rate thresholds of 1.0% (FDR 0.01) were computed for each cell type by applying\
the HotSpot algorithm to an equivalent number of random uniquely\
mapping 36-mers.  DNaseI hypersensitive sites (DHSs or <I>Peaks</I>)\
were identified as signal peaks within 1.0% (FDR 0.01) hypersensitive zones\
using a peak-finding algorithm.  Only DNase Solexa libraries from unique\
cell types producing the highest quality data, as defined by Percent\
Tags in Hotspots (PTIH ~40%), were designated for deep sequencing to a depth\
of over 200 million tags. \
</p>\
\
<h2>Verification</h2>\
\
<p>\
Results were validated by \
conventional DNaseI hypersensitivity assays using end-labeling/Southern \
blotting methods. \
</p>\
\
<h2>Release Notes</h2>\
\
<p>\
This is Release 1 (Aug 2012) of this track, which contains a total of 22 DNaseI\
Digital Genomic Footprinting (DNaseI DGF) experiments.\
</p>\
\
<H2>Credits</H2>\
\
<P>These data were generated by the UW ENCODE group. </P>\
<P>Contact: <A HREF="mailto:&#115;&#117;l&#108;&#64;&#117;.w&#97;&#115;h&#105;&#110;&#103;&#116;&#111;n.&#101;&#100;&#117;">\
Richard Sandstrom</A>\
<!-- above address is sull at u.washington.edu -->\
</P>\
\
<H2>References</H2>\
\
<p>\
Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner MO <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/15550541" target="_blank">\
Discovery of functional noncoding elements by digital analysis of chromatin structure</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2004 Nov 30;101(48):16837-42.\
</p>\
\
<p>\
Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/16791208" target="_blank">\
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays</a>.\
<em>Nat Methods</em>. 2006 Jul;3(7):511-8.\
</p>\
\
<H2> Data Release Policy </H2>\
\
Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an \
unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in \
the <em>Restricted Until</em> column, above. \
The full data release policy for ENCODE is available <a href="/ENCODE/terms.html" target="_blank">here</a>.\
	regulation	1	compositeTrack on\
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dimensions dimensionX=cellType dimensionY=age dimensionA=strain dimensionB=rep\
dragAndDrop subTracks\
fileSortOrder cell=Cell_Line treatment=Treatment strain=Strain age=Age replicate=Replicate view=View geoSampleAccession=GEO_Sample<BR>Accession fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until\
filterComposite dimensionA=multi dimensionB=all\
group regulation\
html wgEncodeUwDgf\
longLabel DNaseI Digital Genomic Footprinting from ENCODE/University of Washington\
noInherit on\
priority 0\
shortLabel UW DNaseI DGF\
sortOrder cellType=+ treatment=+ age=+ strain=+ rep=+ view=+\
subGroup1 view Views Hotspots=Hotspots Peaks=Peaks Signal=Signal RawSignal=Raw_Signal\
subGroup2 cellType Cell_Line Cel3134=3134 Cel416B=416B CelA20=A20 CelBCELLCD19P=B-cell_(CD19+) CelBCELLCD43N=B-cell_(CD43-) CBELLUM=Cerebellum CEREBRUM=Cerebrum ESCJ7=ES-CJ7 FAT=FatPad FIBROBLAST=Fibroblast FLBUD=ForelimbBud GFAT=GenitalFatPad HEART=Heart HLBUD=HindlimbBud KIDNEY=Kidney LIVER=Liver LUNG=Lung MEL=MEL NIH3T3=NIH-3T3 RETINA=Retina THELPA=THelper-Activated THYMUS=Thymus TNAIVE=T-Naive TREG=TReg TREGA=TReg-Activated WBRAIN=Whole_Brain ZHBTC4=ZhBTc4\
subGroup3 strain Strain A129=129 A129OLA=129/Ola A129S1=129S1/SVImJ BALBCANN=BALB/cAnN B6D2F1J=B6D2F1/J C57BL6=C57BL/6 CD1=CD-1 NIHS=NIH/Swiss RIII=RIII SPBL6=Spretus.BL6-Xist  UKN=Unknown\
subGroup4 age Age ADULT8WKS=Adult_8_Weeks E0=Embryonic_Day_0 E11HALF=E11.5 E14HALF=Embryonic_Day_14.5 E18HALF=E18.5 IMMORTAL=Immortalized NEW1DAYS=Newborn_1_Day\
subGroup5 rep Replicate rep1=1 rep2=2\
subGroup6 treatment Treatment NONE=None DIFFB24H=24_hour_diff_protocol_B\
track wgEncodeUwDgf\
type bed 3\

wgEncodeUwDnase	UW DNaseI HS	bed 3	DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington	0	100	0	0	0	127	127	127	0	0	0			<h2>Description</h2>\
\
<p>\
This track was produced as part of the mouse ENCODE Project.\
It shows DNaseI sensitivity measured genome-wide in mouse\
<a href="/cgi-bin/hgEncodeVocab?type=cellType" target="_blank">tissues and cell lines</a>\
using the Digital DNaseI methodology (see below), and DNaseI hypersensitive\
sites. DNaseI has long been used to map general chromatin accessibility and\
DNaseI hypersensitivity is a universal feature of active\
<em>cis</em>-regulatory sequences. The use of this method has led\
to the discovery of functional regulatory elements that include enhancers,\
insulators, promoters, locus control regions and novel elements.\
For each experiment (tissue/cell type), this track shows DNaseI sensitivity as a\
continuous function using sequencing tag density (<em>Signal</em>),\
and discrete loci of DNaseI sensitive zones (<em>HotSpots</em>) and\
hypersensitive sites (<em>Peaks</em>).\
</p>\
\
<h2>Display Conventions and Configuration</h2>\
\
<p>\
This track is a multi-view composite track that contains multiple data types\
(<em>views</em>). For each view, there are multiple subtracks that display\
individually on the browser. Instructions for configuring multi-view tracks\
are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
This track contains the following views:\
</p>\
\
<dl>\
<dt><em>HotSpots</em></dt>\
<dd> DNaseI sensitive zones identified using the HotSpot algorithm.</dd>\
<dt><em>Peaks</em></dt>\
<dd> DNaseI hypersensitive sites (DHSs) identified as signal peaks within\
FDR 1.0% hypersensitive zones.</dd>\
<dt><em>Signal</em></dt>\
<dd>The density of tags mapping within a 150 bp sliding window\
(at a 20 bp step across the genome).</dd>\
</dl>\
\
<p>\
DNaseI sensitivity is shown as the absolute density of <em>in vivo</em>\
cleavage sites across the genome mapped using the Digital DNaseI methodology\
(see below). Data have been normalized to 25 million reads per cell type.\
</p>\
\
<p>\
Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.\
</p>\
\
<H2>Methods</H2>\
\
<p>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
Fresh tissues were harvested from mice and the nuclei prepared according\
to the tissue-appropriate\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">protocol</a>.\
Digital DNaseI was performed by DNaseI digestion of intact\
nuclei, isolating DNaseI 'double-hit' fragments as described in\
Sabo <em>et al</em>. (2006), and direct sequencing of fragment\
ends (which correspond to <em>in vivo</em> DNaseI cleavage sites)\
using the Illumina IIx (and Illumina HiSeq by early 2011) platform (36 bp reads).\
Uniquely-mapping high-quality reads were mapped to the genome using\
<a href="http://bowtie-bio.sourceforge.net/index.shtml" target="_blank">Bowtie</a>.\
DNaseI sensitivity is directly reflected in\
raw tag density, which is shown in the track as density of tags\
mapping within a 150 bp sliding window (at a 20 bp step across the genome).\
DNaseI sensitive zones (<em>HotSpots</em>) were identified using the\
HotSpot algorithm described in Sabo <em>et al</em>. (2004). False discovery\
rate thresholds of 1.0% (FDR 1.0%) were computed for each cell type by\
applying the HotSpot algorithm to an equivalent number of random\
uniquely-mapping 36mers.  DNaseI hypersensitive sites (DHSs or <em>Peaks</em>)\
were identified as signal peaks within FDR 1.0% hypersensitive\
zones using a peak-finding algorithm (<em>I-max</em>).\
</p>\
\
<h2>Verification</h2>\
\
<p>\
Data were verified by sequencing biological replicates displaying\
correlation coefficient &gt; 0.9.\
</p>\
\
<h2>Release Notes</h2>\
\
<p>\
This is Release 2 (September 2012) of this track. It adds 32 new experiments including 22 new cell lines and 4 new treatments.\
</p>\
\
<H2>Credits</H2>\
\
<p>\
These data were generated by the UW ENCODE group.\
</p>\
\
<p>\
Contact: <a href="mailto:&#115;&#117;l&#108;&#64;&#117;.w&#97;&#115;h&#105;&#110;&#103;&#116;&#111;n.&#101;&#100;&#117;">\
Richard Sandstrom</a>\
<!-- above address is sull at u.washington.edu -->\
</p>\
\
<h2>References</h2>\
\
<p>\
John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/21258342" target="_blank">\
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns</a>.\
<em>Nat Genet</em>. 2011 Mar;43(3):264-8.\
</p>\
\
<p>\
Sabo PJ, Hawrylycz M, Wallace JC, Humbert R, Yu M, Shafer A, Kawamoto J, Hall R, Mack J, Dorschner\
MO <em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/15550541" target="_blank">\
Discovery of functional noncoding elements by digital analysis of chromatin structure</a>.\
<em>Proc Natl Acad Sci U S A</em>. 2004 Nov 30;101(48):16837-42.\
</p>\
\
<p>\
Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, Cao H, Yu M, Rosenzweig E, Goldy J, Haydock A\
<em>et al</em>.\
<a href="https://www.ncbi.nlm.nih.gov/pubmed/16791208" target="_blank">\
Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays</a>.\
<em>Nat Methods</em>. 2006 Jul;3(7):511-8.\
</p>\
\
<h2>Data Release Policy</h2>\
\
<p>\
Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <em>Restricted Until</em> column, above.  The full data release policy\
for ENCODE is available\
<a href="/ENCODE/terms.html" target="_blank">here</a>.\
</p>\
	regulation	1	compositeTrack on\
controlledVocabulary encode/cv.ra cellType=cell strain=strain age=age sex=sex treatment=Treatment\
dimensionCchecked rep1\
dimensions dimensionX=cellType dimensionY=age dimensionA=strain dimensionB=treatment dimesionC=rep\
dragAndDrop subTracks\
fileSortOrder cell=Cell_Line strain=Strain age=Age treatment=Treatment sex=Sex replicate=Replicate view=View dccAccession=UCSC_Accession geoSampleAccession=GEO_Accession fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until\
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group regulation\
html wgEncodeUwDnase.release2\
longLabel DNaseI Hypersensitivity by Digital DNaseI from ENCODE/University of Washington\
noInherit on\
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shortLabel UW DNaseI HS\
sortOrder cellType=+ strain=+ age=+ treatment=+ sex=+ rep=+ view=+\
subGroup1 view Views Hotspots=Hotspots Peaks=Peaks Signal=Signal\
subGroup2 cellType Cell_Line A13134=3134 A1416B=416B A20=A20 BCELLCD19P=B-cell_(CD19+) BCELLCD43N=B-cell_(CD43-) CBELLUM=Cerebellum CEREBRUM=Cerebrum CH12=CH12 EPCMPP=EPC_(CD117-,CD71+,TER119+) EPCPMM=EPC_(CD117+,CD71-,TER119-) EPCPPM=EPC_(CD117+,CD71+,TER119-) EPCPPP=EPC_(CD117+,CD71+,TER119+) ESCJ7=ES-CJ7 ESE14=ES-E14 ESWW6=ES-WW6 ESWW6KO=ES-WW6_F1KO FAT=Fat_Pad FIBROBLAST=Fibroblast FLBUD=Fore_Limb_Bud GFAT=Genital_Fat_Pad HEADLEMBRYO=Headless_Embryo HEART=Heart HLBUD=Hind_Limb_Bud KIDNEY=Kidney LGINT=Large_Intestine LIVER=Liver LUNG=Lung MEL=MEL MESODERM=Mesoderm MGER=mG/ER NIH3T3=NIH-3T3 PATSKI=Patski RETINA=Retina SKMUSCLE=Skeletal_Muscle SPLEEN=Spleen T1NAIVE=T-Naive THELPA=THelper-Activated THYMUS=Thymus TREG=TReg TREGA=TReg-Activated WBRAIN=Whole_Brain ZHBTC4=ZhBTc4\
subGroup3 strain Strain b2A4B=B10.H-2aH-4bp/Wts BALBCANN=BALB/cAnN B6D2F1J=B6D2F1/J C57BL6=C57BL/6 CD1=CD-1 NIHS=NIH/Swiss RIII=RIII a129=129 a129DLCR=129.DLCR/DLCR a129OLA=129/Ola a129S1=129S1/SVImJ SPBL6=Spretus.BL6-Xist  UKN=Unknown\
subGroup4 sex Sex F=F M=M U=U\
subGroup5 age Age ADULT1WKS=Adult_1_Week ADULT8WKS=Adult_8_Weeks E0=Embryonic_Day_0 E11HALF=Embryonic_Day_11.5 E14HALF=Embryonic_Day_14.5 E18HALF=Embryonic_Day_18.5 IMMORTAL=Immortalized NEW1DAYS=Newborn_1_day\
subGroup6 rep Replicate rep1=1 rep2=2 rep3=3 rep4=4 rep5=5 rep6=6 rep7=7 rep8=8 rep9=9 rep10=10 rep11=11 rep12=12 rep13=13 rep14=14\
subGroup7 treatment Treatment DIFFB24H=diffProtB_24_hr DIFFB6H=diffProtB_6_hr DIFFC24H=diffProtC_24_hr DIFFC48H=diffProtC_48_hr zNONE=None\
track wgEncodeUwDnase\
type bed 3\

wgEncodeUwRnaSeq	UW RNA-seq	bed 3	RNA-seq from ENCODE/UW	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
\
<p>This track was produced as part of the mouse ENCODE Project.\
This track shows RNA-seq measured genome-wide in mouse\
<A TARGET=_BLANK HREF="/cgi-bin/hgEncodeVocab?type=cellType"> tissues and cell lines</A>.\
Poly-A selected mRNA was used as the source for transcriptome profiling of tissues and cell types \
that also had corresponding DNase I hypersensitive profiles.\
</p>\
\
<H2>Display Conventions and Configuration</H2>\
<p>\
This track is a multi-view composite track that contains multiple data types (<EM>views</EM>). \
For each view, there are multiple subtracks that display individually on the browser. Instructions \
for configuring multi-view tracks are <a href="/goldenPath/help/multiView.html" target="_blank">here</a>.\
Color differences among the views are arbitrary and they provide a visual cue for distinguishing\
between the different cell and tissue types.  This track contains the following views:\
<DL>\
<DT><I>Plus</I> and <I>Minus</I> <I>Signals</I><DD>These views display clusters of overlapping read mappings \
on the forward and reverse genomic strands.<DD> \
<DT><I>Signal</I></DT><DD>Density graph (wiggle) of signal enrichment based on processed data.</DD>\
<DT><I>Alignments</I></DT><DD>Mappings of short 50-base single end reads to the genome.  See the <A HREF="https://samtools.github.io/hts-specs/SAMv1.pdf" TARGET="_BLANK">SAM Format Specification</A> for more information on the SAM/BAM file format. <DD>\
</DL>\
\
<H2>Methods</H2>\
<p>\
Cells were grown according to the approved\
<a href="/ENCODE/protocols/cell/mouse" target="_blank">ENCODE cell culture protocols</a>.\
Fresh tissues were harvested from mice and stored until used for preparing total RNA samples.  The total RNA \
was used as starting material to select poly-A RNA and used for constructing SOLiD libraries according to the \
protocols supplied by the manufacturer.  All RNA samples were spiked in with NIST standards before libraries were constructed.\
 The RNA-seq libraries were sequenced on ABI SOLiD sequencing platform as 50-base reads according to the manufacturer's recommendations.\
<p>\
Reads were aligned to the mm9 reference genome using ABI BioScope software version 1.2.1.  Colorspace FASTQ format files were created \
using Heng Li's solid2fastq.pl script version 0.1.4 (Li <EM>et al.</EM>, 2009a), representing 0, 1, 2, 3 color codes with the letters A, C, G, T respectively.  \
 Signal files were created from the BAM (Li <EM>et al.</EM>, 2009b) alignments using BEDTools (Quinlan <EM>et al.</EM>, 2010). \
</p>\
\
<h2>Release Notes</h2>\
\
<p>\
This is Release 1 (July 2012). It contains a total of 25 RNA-seq experiments.\
</p>\
\
\
<H2>Credits</H2>\
\
<p>These data were generated by the UW ENCODE group. </p>\
<p>Contact: <A HREF="mailto:&#115;&#117;l&#108;&#64;&#117;.w&#97;&#115;h&#105;&#110;&#103;&#116;&#111;n.&#101;&#100;&#117;">\
Richard Sandstrom</A>\
<!-- above address is sull at u.washington.edu -->\
</p>\
\
<H2>References</H2>\
\
<p>\
Li H, Durbin R.\
<a href="https://academic.oup.com/bioinformatics/article/25/14/1754/225615"\
target="_blank">\
Fast and accurate short read alignment with Burrows-Wheeler transform</a>.\
<em>Bioinformatics</em>. 2009 Jul 15;25(14):1754-60.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19451168" target="_blank">19451168</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234/" target="_blank">PMC2705234</a>\
</p>\
\
<p>\
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome\
Project Data Processing Subgroup.\
<a href="https://academic.oup.com/bioinformatics/article/25/16/2078/204688"\
target="_blank">\
The Sequence Alignment/Map format and SAMtools</a>.\
<em>Bioinformatics</em>. 2009 Aug 15;25(16):2078-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19505943" target="_blank">19505943</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002/" target="_blank">PMC2723002</a>\
</p>\
\
<p>\
Quinlan AR, Hall IM.\
<a href="https://academic.oup.com/bioinformatics/article/26/6/841/244688" target="_blank">\
BEDTools: a flexible suite of utilities for comparing genomic features</a>.\
<em>Bioinformatics</em>. 2010 Mar 15;26(6):841-2.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20110278" target="_blank">20110278</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832824/" target="_blank">PMC2832824</a>\
</p>\
\
<H2> Data Release Policy </H2>\
\
<p>Data users may freely use ENCODE data, but may not, without prior\
consent, submit publications that use an unpublished ENCODE dataset until\
nine months following the release of the dataset.  This date is listed in\
the <EM>Restricted Until</EM> column, above.  The full data release policy\
for ENCODE is available\
<A TARGET=_BLANK HREF="../ENCODE/terms.html" TARGET=_BLANK> here</A>.</p>\
\
	regulation	1	compositeTrack on\
controlledVocabulary encode/cv.ra cellType=cell localization=localization rnaExtract=rnaExtract sex=sex age=age strain=strain\
dimensions dimensionX=cellType dimensionY=age dimensionA=rep dimensionB=strain\
dragAndDrop subTracks\
fileSortOrder cell=Cell_Line strain=Strain view=View replicate=Replicate age=Age dccAccession=UCSC_Accession geoSampleAccession=GEO_Accession fileSize=Size fileType=File_Type dateSubmitted=Submitted dateUnrestricted=RESTRICTED<BR>Until\
filterComposite dimA=multi dimB=multi\
group regulation\
html wgEncodeUwRnaSeq\
longLabel RNA-seq from ENCODE/UW\
noInherit on\
priority 0\
shortLabel UW RNA-seq\
sortOrder cellType=+ view=+ rep=+ age=+ strain=+ sex=+\
subGroup1 view Views Signal=Signal Alignments=Alignments PlusRawSignal=Plus_Raw_Signal MinusRawSignal=Minus_Raw_Signal\
subGroup2 cellType Cell_Line ACel416B=416B A20=A20 BCELLCD19P=B-cell_(CD19+) BCELLCD43N=B-cell_(CD43-) CBELLUM=Cerebellum CEREBRUM=Cerebrum FAT=FatPad GFAT=GenitalFatPad H1LEMBRYO=HeadlessEmbryo H2EART=Heart KIDNEY=Kidney LGINT=Large_Intestine LIVER=Liver LUNG=Lung  MEL=MEL NIH3T3=NIH-3T3 PATSKI=Patski SKMUSCLE=Skeletal_Muscle SPLEEN=Spleen T1NAIVE=T-Naive T2HYMUS=Thymus WBRAIN=Whole_Brain\
subGroup3 localization Localization CELL=cell\
subGroup4 rnaExtract RnaExtract POLYA=polyA\
subGroup5 rep Replicate rep1=1 rep2=2 rep3=3 rep4=4\
subGroup6 sex Sex M=M F=F\
subGroup7 age Age ADULT8WKS=adult-8wks E11HALF=E11.5 E14HALF=E14.5 E18HALF=E18.5 IMMORTAL=immortalized\
subGroup8 strain Strain BALBCANN=BALB/cAnN B6D2F1J=B6D2F1/J C57BL6=C57BL/6 CD1=CD-1 NIHS=NIH/Swiss A1S129=129 SPBL6=Spretus.BL6-Xist UKN=Unknown\
track wgEncodeUwRnaSeq\
type bed 3\

vegaGeneComposite	Vega Genes	genePred vegaPep	Vega Annotations	0	100	0	0	0	127	127	127	0	0	21	chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY,	http://vega.sanger.ac.uk/Mus_musculus/transview?transcript=$$	<H2>Description and Methods </H2>\
\
<P>\
This track shows gene annotations from the Vertebrate Genome Annotation (Vega)\
database. Annotations are divided into two subtracks from the\
<A HREF="http://vega.archive.ensembl.org/Mus_musculus/Info/Indexh"\
TARGET=_BLANK>Vega Mouse Genome Annotation</A> project:\
<UL>\
 <LI>Vega Protein Coding Annotations\
 <LI>Vega Annotated Pseudogenes and Immunoglobulin Segments\
</UL>\
\
<P>\
The following information is an excerpt from the\
<A HREF="http://vega.archive.ensembl.org/index.html" TARGET=_BLANK>\
Vertebrate Genome Annotation</A> home page:</P>\
<P>\
&quot;The Vega database\
is designed to be a central repository for high-quality, frequently updated\
manual annotation of different vertebrate finished genome sequence.\
Vega attempts to present consistent high-quality curation of the published\
chromosome sequences. Finished genomic sequence is analysed on a\
clone-by-clone basis using\
a combination of similarity searches against DNA and protein databases\
as well as a series of <em>ab initio</em> gene predictions (GENSCAN, Fgenes).\
The annotation is based on supporting evidence only.&quot;</P>\
<P>\
&quot;In addition, comparative analysis using vertebrate datasets such as\
the Riken mouse cDNAs and Genoscope <em>Tetraodon nigroviridis</em> Ecores\
(Evolutionary Conserved Regions) are used for novel gene discovery.&quot;</P>\
<P>\
\
<H2>Display Conventions and Configuration</H2>\
<P>\
This track follows the display conventions for\
<A HREF="../goldenPath/help/hgTracksHelp.html#GeneDisplay">gene prediction\
tracks</A>. Transcript\
type (and other details) may be found by clicking on the transcript\
identifier which forms the outside link to the Vega transcript details page.\
Further information on the gene and transcript classification may be found\
<A HREF="http://vega.archive.ensembl.org/info/about/gene_and_transcript_types.html"\
TARGET=_blank>here</A>.\
</P>\
\
<H2> Credits </H2>\
<P>\
Thanks to Steve Trevanion at the\
<A HREF="https://www.sanger.ac.uk/" TARGET=_BLANK>\
Wellcome Trust Sanger Institute</A> \
for providing the GTF and FASTA files for the Vega annotations. Vega \
acknowledgements and publications are listed \
<A HREF="http://vega.archive.ensembl.org/info/acknowledgements/Mus_musculus.html" \
TARGET=_BLANK>here</A>.\
	genes	1	chromosomes chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chrX,chrY\
compositeTrack on\
exonNumbers on\
group genes\
longLabel Vega Annotations\
shortLabel Vega Genes\
track vegaGeneComposite\
type genePred vegaPep\
url http://vega.sanger.ac.uk/Mus_musculus/transview?transcript=$$\
urlLabel Vega Transcript:\
visibility hide\

vistaEnhancersBb	VISTA Enhancers	bigBed 9 +	VISTA Enhancers	0	100	0	0	0	127	127	127	0	0	0		https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=presentation&show=1&organism_id=2&experiment_id=$<experimentId>	<H2>Description</H2>\
\
<p>This track shows potential enhancers whose activity was experimentally validated in transgenic\
mice. Most of these noncoding elements were selected for testing based on their extreme conservation\
in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. More information\
can be found on the <a href="http://enhancer.lbl.gov" target="_blank">VISTA Enhancer Browser</a>\
page.\
</p>\
\
<h2> Display Conventions and Configuration </h2>\
<p> Items appearing in <b><font color="red">red</font></b> (positive) indicate that a reproducible\
pattern was observed in the in vivo enhancer assay. Items appearing in\
<b><font color="blue">blue</font></b> (negative) indicate that NO reproducible pattern was observed\
in the  in vivo enhancer assay.  Note that this annotation refers only to the single developmental\
timepoint that was tested in this screen (e11.5) and does not exclude the possibility that this\
region is a reproducible enhancer active at earlier or later timepoints in development.\
</p>\
\
<h2>Methods</h2>\
<p> Excerpted from the Vista Enhancer <a HREF="https://enhancer.lbl.gov/aboutproject_n.html"\
TARGET=_BLANK>Mouse Enhancer Screen Handbook and Methods</a> page at the Lawrence Berkeley\
National Laboratory (LBNL) website:\
<h4>Enhancer Candidate Identification</h4>\
<p> Most enhancer candidate sequences are identified by extreme evolutionary sequence conservation or\
by ChIP-seq.  Detailed information related to enhancer identification by extreme evolutionary\
conservation can be found in the following publications:\
</p>\
<ul>\
<li>Pennacchio et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/11253049" target="_blank"\
>Genomic strategies to identify mammalian regulatory sequences.</a> Nature Rev Genet 2001</li>\
<li>Nobrega et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/14563999" target="_blank"\
>Nobrega et al., Scanning human gene deserts for long-range enhancers.</a> Science 2003</li>\
<li>Pennacchio et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/17086198" target="_blank"\
>In vivo enhancer analysis of human conserved non-coding sequences.</a> Nature 2006</li>\
<li>Visel et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/17276707" target="_blank"\
>Enhancer identification through comparative genomics.</a> Semin Cell Dev Biol. 2007</li>\
<li>Visel et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/18176564" target="_blank"\
>Ultraconservation identifies a small subset of extremely constrained developmental enhancers.</a>\
 Nature Genet 2008</li>\
</ul>\
\
<p>Detailed information related to enhancer identification by ChIP-seq can be found in the\
following publications:</p>\
<ul>\
<li>Visel et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/19212405" target="_blank"\
>ChIP-seq accurately predicts tissue-specific activity of enhancers.</a> Nature 2009</li>\
<li>Visel et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/19741700" target="_blank"\
>Genomic views of distant-acting enhancers.</a> Nature 2009</li>\
</ul></p>\
\
<p>See the Transgenic Mouse Assay section for experimental procedures that were used to perform the\
transgenic assays: <a HREF="https://enhancer.lbl.gov/aboutproject_n.html"\
TARGET=_BLANK>Mouse Enhancer Screen Handbook and Methods</a> \
\
<p>UCSC converted the\
<a href="https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?show=1;page=1;search.form=no;page_size=20000;action=search;form=search;search.result=yes;search.sequence=1"\
target="_blank">Experimental Data</a> for hg19 and mm9 into bigBed format using the bedToBigBed\
utility. The data for hg38 was lifted over from hg19. The data for mm10 and mm39 were lifted over\
from mm9.</p> \
\
<h2>Data Access</h2>\
<p>\
VISTA Enhancers data can be explored interactively with the\
<a href="../cgi-bin/hgTables">Table Browser</a> and cross-referenced with the\
<a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, the track can be\
accessed using the Genome Browser's <a href="/goldenPath/help/api.html">REST API</a>. ReMap\
annotations can be downloaded from the Genome Browser's\
<a href="https://hgdownload.soe.ucsc.edu/gbdb/mm9/vistaEnhancers">download server</a>\
as a bigBed file. This compressed binary format can be remotely queried through\
command line utilities. Please note that some of the download files can be quite large.</p>\
\
<h2>Credits</h2>\
<p>Thanks to the Lawrence Berkeley National Laboratory for providing this data</p>\
\
\
<h2>References</h2>\
<p>\
Visel A, Minovitsky S, Dubchak I, Pennacchio LA.\
<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkl822" target="_blank">\
VISTA Enhancer Browser--a database of tissue-specific human enhancers</a>.\
<em>Nucleic Acids Res</em>. 2007 Jan;35(Database issue):D88-92.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17130149" target="_blank">17130149</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716724/" target="_blank">PMC1716724</a>\
</p>\
	regulation	1	bigDataUrl /gbdb/mm9/vistaEnhancers/vistaEnhancers.bb\
group regulation\
itemRgb on\
longLabel VISTA Enhancers\
pennantIcon New red ../goldenPath/newsarch.html#120723 "Released Dec. 7, 2023"\
shortLabel VISTA Enhancers\
track vistaEnhancersBb\
type bigBed 9 +\
url https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=presentation&show=1&organism_id=2&experiment_id=$<experimentId>\
urlLabel View on the VISTA Enhancer Browser\

pubsBingBlat	Web Sequences	bed 12 +	DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research	0	100	0	0	0	127	127	127	0	0	0			<H2>Description</H2>\
<P>This track is powered by Bing! and Microsoft Research. UCSC collaborators at\
Microsoft Research (Bob Davidson, David Heckerman) implemented a DNA sequence\
detector and processed thirty days of web crawler updates, which covers\
roughly 40 billion webpages. The results were mapped with BLAT to the genome.</P>\
\
<H2>Display Convention and Configuration</H2>\
<P>The track indicates the location of sequences on web pages\
mapped to the genome, labelled with the web page URL. If the web page includes\
invisible meta data, then the first author and a year of publication \
is shown instead of the URL.  All\
matches of one web page are grouped (&quot;chained&quot;) together.\
Web page titles are shown when you move the mouse cursor over the features.\
Thicker parts of the features (exons) represent matching sequences,\
connected by thin lines to matches from the same web page within 30 kbp.</P>\
\
<!-- Feature not active at this time ============================================\
<P>The subtrack "individual sequence matches" activates automatically when\
the user clicks a sequence match and follows the link "Show sequence matches individually" \
from the details page.  Mouse-overs show flanking text around the sequence, and clicking\
features links to BLAT alignments.\
</P>\
- -->\
\
<H2>Methods</H2>\
<P>\
All file types (PDFs and various Microsoft Office formats) were converted to\
text. The results were processed to find groups of words that look like DNA/RNA\
sequences. These were then mapped with BLAT to the human genome using the same\
software as used in the <a href="hgTrackUi?g=pubs">Publication track</a>.</P>\
\
<H2>Credits</H2>\
<P>DNA sequence detection by Bob Davidson at Microsoft Research. \
HTML parsing and sequence mapping by Maximilian Haeussler at UCSC.</P>\
\
<H2>References</H2>\
\
<p>\
Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM, Open Regulatory Annotation Consortium.\
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-2-r31" target="_blank">\
Text-mining assisted regulatory annotation</a>.\
<em>Genome Biol</em>. 2008;9(2):R31.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/18271954" target="_blank">18271954</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374703/" target="_blank">PMC2374703</a>\
</p>\
\
<p>\
Haeussler M, Gerner M, Bergman CM.\
<a href="https://academic.oup.com/bioinformatics/article/27/7/980/230859/Annotating-genes-and-genomes-with-DNA-sequences" target="_blank">\
Annotating genes and genomes with DNA sequences extracted from biomedical articles</a>.\
<em>Bioinformatics</em>. 2011 Apr 1;27(7):980-6.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21325301" target="_blank">21325301</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3065681/" target="_blank">PMC3065681</a>\
</p>\
\
<p>\
Van Noorden R.\
<a href="https://www.nature.com/news/trouble-at-the-text-mine-1.10184" target="_blank">\
Trouble at the text mine</a>.\
<em>Nature</em>. 2012 Mar 7;483(7388):134-5.\
</p>\
	pub	1	configurable off\
configureByPopup off\
group pub\
longLabel DNA Sequences in Web Pages Indexed by Bing.com / Microsoft Research\
nextExonText Next Match\
prevExonText Prev Match\
pubsArticleTable hgFixed.pubsBingArticle\
pubsMarkerTable hgFixed.pubsBingMarkerAnnot\
pubsPslTrack pubsBingBlatPsl\
pubsSequenceTable hgFixed.pubsBingSequenceAnnot\
shortLabel Web Sequences\
track pubsBingBlat\
type bed 12 +\
visibility hide\

pseudoYale60	Yale Pseudo60	genePred	Yale Pseudogenes based on Ensembl Release 60	0	100	0	0	0	127	127	127	1	0	0		http://tables.pseudogene.org/index.cgi?table=Mouse60&value=$$	<h2>Description</h2>\
\
<p>\
This track shows pseudogenes identified by the Yale Pseudogene Pipeline.  \
Pseudogenes are defined in this analysis as genomic sequences that are \
similar to known genes with various inactivating disablements (e.g., premature \
stop codons or frameshifts) in their &quot;putative&quot; protein coding regions. \
Pseudogenes are flagged as either recently processed, recently duplicated, \
or of uncertain origin (either ancient fragments or resulting from a \
single-exon parent). NOTE: There are 4 pseudogenes missing - these had \
overlapping coordinates in the blocks representing exons and their \
identifiers are:\
</p>\
\
<ul>\
<li>PGOMOU00000130313</li>\
<li>PGOMOU00000139101</li>\
<li>PGOMOU00000136201</li>\
<li>PGOMOU00000128816</li>\
</ul>\
\
<h2>Methods</h2>\
\
<p>\
Briefly, the protein sequences of known human genes (as annotated by Ensembl Release\
60) were used to search for similarities, not overlapping with known genes.\
It was determined whether the matching sequences were disabled copies of genes \
based on the occurrences of premature stop codons or frameshifts.  The\
intron-exon structure of the functional gene was further used to infer\
whether a pseudogene was recently duplicated or processed. A duplicated\
pseudogene retains the intron-exon structure of its parent functional\
gene, whereas a processed pseudogene shows evidence that this structure \
has been spliced out. Small pseudogene sequences that cannot be confidently \
assigned to either the processed or duplicated category may be ancient \
fragments. Further details are in the references below. \
</p>\
\
<h2>Credits</h2>\
\
<p>\
These data were generated by the pseudogene annotation group in the \
<a href="http://www.gersteinlab.org/" target="_blank">Gerstein Lab</a> at Yale University.\
</p>\
\
<h2>References</h2>\
\
<p>\
More information is available from\
<a href="http://www.pseudogene.org/" target="_blank">Pseudogene.org</a>.\
</p>\
\
<p>\
Zhang Z, Harrison PM, Liu Y, Gerstein M.\
<a href="https://genome.cshlp.org/content/13/12/2541.long" target="_blank">\
Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in\
the human genome</a>.\
<em>Genome Res</em>. 2003 Dec;13(12):2541-58.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14656962" target="_blank">14656962</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC403796/" target="_blank">PMC403796</a>\
</p>\
\
<p>\
Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M.\
<a href="https://www.sciencedirect.com/science/article/pii/S0022283605003025" target="_blank">\
Integrated pseudogene annotation for human chromosome 22: evidence for transcription</a>.\
<em>J Mol Biol</em>. 2005 May 27;349(1):27-45.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15876366" target="_blank">15876366</a>\
</p>\
	genes	1	autoTranslate 0\
dataVersion December 2010\
gClass_Ambiguous 100,91,191\
gClass_Duplicated 100,50,0\
gClass_Processed 180,0,0\
geneClasses Processed Duplicated Ambiguous\
group genes\
itemClassTbl pseudoYale60Class\
longLabel Yale Pseudogenes based on Ensembl Release 60\
shortLabel Yale Pseudo60\
spectrum on\
track pseudoYale60\
type genePred\
url http://tables.pseudogene.org/index.cgi?table=Mouse60&value=$$\
urlLabel Yale pseudogene.org link:\
visibility hide\

wgEncodeUwDnaseFlbudCd1ME11halfPkRep2	Fore Limb Bud P 2	narrowPeak	Fore Limb Bud DNaseI HS Peaks Rep 2 from ENCODE/UW	3	101	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Fore Limb Bud DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Fore Limb Bud P 2\
subGroups view=Peaks age=E11HALF cellType=FLBUD sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseFlbudCd1ME11halfPkRep2\
type narrowPeak\

wgEncodeLicrHistoneHeartH3k79me2MAdult8wksC57bl6StdPk	Heart 8w H3K79m2	broadPeak	Heart 8w H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	101	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart 8w H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Heart 8w H3K79m2\
subGroups view=Peaks age=A1DLT8W factor=H3K79ME2 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k79me2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep2	Kidney - 2	bigWig 1.000000 1498409.000000	Kidney A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	101	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel Kidney - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=KIDNEY rep=rep2\
track wgEncodeCshlLongRnaSeqKidneyAdult8wksMinusRawRep2\
type bigWig 1.000000 1498409.000000\

wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep1	MEL A 1	bam	MEL Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW	0	101	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel MEL A 1\
subGroups view=Alignments age=IMMORTAL cellType=MEL localization=CELL rnaExtract=POLYA sex=M strain=UKN rep=rep1\
track wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep1\
type bam\

wgEncodeSydhTfbsMelMafkDm2p5dStdSig	MEL MafK_a D	bigWig 1.000000 40202.000000	MEL MafK (ab50322) DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	101	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL MafK (ab50322) DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL MafK_a D\
subGroups view=Signal factor=MAFKAB50322 cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhTfbsMelMafkDm2p5dStdSig\
type bigWig 1.000000 40202.000000\

wgEncodeUwDnaseFlbudCd1ME11halfSigRep2	Fore Limb Bud S 2	bigWig 1.000000 396503.000000	Fore Limb Bud DNaseI HS Signal Rep 2 from ENCODE/UW	2	102	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Fore Limb Bud DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Fore Limb Bud S 2\
subGroups view=Signal age=E11HALF cellType=FLBUD sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseFlbudCd1ME11halfSigRep2\
type bigWig 1.000000 396503.000000\

wgEncodeLicrHistoneHeartH3k79me2MAdult8wksC57bl6StdSig	Heart 8w H3K79m2	bigWig 0.110000 40.750000	Heart 8w H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	102	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Heart 8w H3K79m2\
subGroups view=Signal age=A1DLT8W factor=H3K79ME2 cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartH3k79me2MAdult8wksC57bl6StdSig\
type bigWig 0.110000 40.750000\
viewLimits 0.2:3\

wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep2	Kidney + 2	bigWig 1.000000 1934001.000000	Kidney A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	102	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Kidney + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=KIDNEY rep=rep2\
track wgEncodeCshlLongRnaSeqKidneyAdult8wksPlusRawRep2\
type bigWig 1.000000 1934001.000000\

wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep2	MEL A 2	bam	MEL Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW	0	102	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel MEL A 2\
subGroups view=Alignments age=IMMORTAL cellType=MEL localization=CELL rnaExtract=POLYA sex=M strain=UKN rep=rep2\
track wgEncodeUwRnaSeqMelCellPolyaMImmortalUknAlnRep2\
type bam\

wgEncodeSydhTfbsMelMafkab50322IggrabPk	MEL MafK_a	narrowPeak	MEL MafK (ab50322) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	102	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL MafK (ab50322) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL MafK_a\
subGroups view=Peaks factor=MAFKAB50322 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelMafkab50322IggrabPk\
type narrowPeak\

wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep1	Gen Fat Pad H 1	broadPeak	Genital Fat Pad DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	103	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Genital Fat Pad DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Gen Fat Pad H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=GFAT sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneHeartInputMAdult8wksC57bl6StdSig	Heart 8w Input	bigWig 0.140000 73.459999	Heart 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	103	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Heart 8w Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=HEART control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneHeartInputMAdult8wksC57bl6StdSig\
type bigWig 0.140000 73.459999\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqKidneyAdult8wksContigs	Kidney C	bed 6 +	Kidney A8 Long RNA-seq Contigs from ENCODE/CSHL	3	103	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs\
shortLabel Kidney C\
subGroups view=Contigs age=ADULT8WKS cellType=KIDNEY rep=repP\
track wgEncodeCshlLongRnaSeqKidneyAdult8wksContigs\
type bed 6 +\

wgEncodeSydhTfbsMelMafkab50322IggrabSig	MEL MafK_a	bigWig 1.000000 120440.000000	MEL MafK (ab50322) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	103	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL MafK (ab50322) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL MafK_a\
subGroups view=Signal factor=MAFKAB50322 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelMafkab50322IggrabSig\
type bigWig 1.000000 120440.000000\

wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep1	MEL MR 1	bigWig 1.000000 200174.000000	MEL Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	103	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel MEL MR 1\
subGroups view=MinusRawSignal age=IMMORTAL cellType=MEL localization=CELL rnaExtract=POLYA sex=M strain=UKN rep=rep1\
track wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep1\
type bigWig 1.000000 200174.000000\

wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep1	Gen Fat Pad P 1	narrowPeak	Genital Fat Pad DNaseI HS Peaks Rep 1 from ENCODE/UW	3	104	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Genital Fat Pad DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Gen Fat Pad P 1\
subGroups view=Peaks age=ADULT8WKS cellType=GFAT sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeLicrHistoneHeartInputUE14halfC57bl6StdSig	Heart 14.5 Input	bigWig 0.140000 48.220001	Heart E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	104	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Heart 14.5 Input\
subGroups view=Signal age=E14HALF factor=INPUT cellType=HEART control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneHeartInputUE14halfC57bl6StdSig\
type bigWig 0.140000 48.220001\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqKidneyAdult8wksJunctions	Kidney J	bed 6 +	Kidney A8 Long RNA-seq Junctions from ENCODE/CSHL	0	104	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Kidney J\
subGroups view=SJunctions age=ADULT8WKS cellType=KIDNEY rep=repP\
track wgEncodeCshlLongRnaSeqKidneyAdult8wksJunctions\
type bed 6 +\

wgEncodeSydhTfbsMelMaxIggrabPk	MEL Max	narrowPeak	MEL Max TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	104	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Max TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL Max\
subGroups view=Peaks factor=MAX cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelMaxIggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep2	MEL MR 2	bigWig 1.000000 57935.000000	MEL Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	104	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig\
shortLabel MEL MR 2\
subGroups view=MinusRawSignal age=IMMORTAL cellType=MEL localization=CELL rnaExtract=POLYA sex=M strain=UKN rep=rep2\
track wgEncodeUwRnaSeqMelCellPolyaMImmortalUknMinusRawRep2\
type bigWig 1.000000 57935.000000\

wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep1	Gen Fat Pad S 1	bigWig 1.000000 47469.000000	Genital Fat Pad DNaseI HS Signal Rep 1 from ENCODE/UW	2	105	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Genital Fat Pad DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Gen Fat Pad S 1\
subGroups view=Signal age=ADULT8WKS cellType=GFAT sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 47469.000000\

allMm9RS_BW	GERP	bigWig -10 5	GERP scores for mammalian alignments	0	105	0	0	0	127	127	127	0	0	0			<h2>Description</h2> \
\
<p>Genomic Evolutionary Rate Profiling (GERP) is a method for producing\
position-specific estimates of evolutionary constraint using maximum likelihood evolutionary rate\
estimation. It also discovers "constrained elements" where multiple positions combine to give a\
signal that is indicative of a putative functional element; this track shows the position-specific\
scores only, not the element predictions. </p> \
\
<p>Constraint intensity at each individual alignment\
position is quantified in terms of a "rejected substitutions" (RS) score, defined as the number of\
substitutions expected under neutrality minus the number of substitutions "observed" at the\
position. This concept was described, and a first implementation of GERP was presented, in Cooper et\
al (2005).  GERP++ as described in Davydov et al (2010) uses a more rigorous set of algorithms to\
calculate site-specific RS scores and to discover evolutionarily constrained elements. </p> \
\
<p>Sites are scored independently. Positive scores represent a substitution deficit (i.e., fewer\
substitutions than the average neutral site) and thus indicate that a site may be under evolutionary\
constraint.  Negative scores indicate that a site is probably evolving neutrally; negative scores\
should not be interpreted as evidence of accelerated rates of evolution because of too many strong\
confounders, such as alignment uncertainty or rate variance. Positive scores scale with the level of\
constraint, such that the greater the score, the greater the level of evolutionary constraint\
inferred to be acting on that site. </p> \
\
<p>We applied GERP, as implemented in the GERP++ software\
package, to quantify the level of evolutionary constraint acting on each site in mm9, based on an\
alignment of 22 mammals to mm9 with a maximum phylogenetic scope of 4.14 substitutions per neutral\
site. Gaps in the alignment are treated as missing data, which means that the number of\
substitutions per neutral site will be less than 4.14 in sites where one or more species has a gap. \
Thus, RS scores range from a maximum of 4.14 down to a below-zero minimum, which we cap at -8.28. RS\
scores will vary with alignment depth and level of sequence conservation. A score of 0 indicates\
that the alignment was too shallow at that position to get a meaningful estimate of constraint.\
Should classification into "constrained" and "unconstrained" sites be desired, a threshold may be\
chosen above which sites are considered "constrained".  In practice, we find that a RS score\
threshold of 2 provides high sensitivity while still strongly enriching for truly constrained sites.\
</p> \
\
<h2>Methods</h2> \
\
<p>Given a multiple sequence alignment and a phylogenetic tree with branch\
lengths representing the neutral rate between the species within that alignment, GERP++ quantifies\
constraint intensity at each individual position in terms of rejected substitutions, the difference\
between the neutral rate and the estimated evolutionary rate at the position.  GERP++ begins with a\
pre-defined neutral tree relating the genomes present within the alignment that supplies both the\
total neutral rate across the entire tree and the relative length of each individual branch.  For\
each alignment column, we estimate a scaling factor, applied uniformly to all branches of the tree,\
that maximizes the probability of the observed nucleotides in the alignment column.  The product of\
the scaling factor and the neutral rate defines the 'observed' rate of evolution at each position.\
GERP++ uses the HKY85 model of evolution with the transition/transversion ratio set to 2.0 and\
nucleotide frequencies estimated from the multiple alignment. </p> \
\
<p>To generate RS scores for\
each position in the mouse genome, we used GERP++ to analyze the TBA alignment of mm9 to 22 other\
mammalian species (the most distant mammalian species being platypus) spanning over 2.5 billion\
positions (see the description for the 'Conservation' track for details of this alignment).  The\
alignment was compressed to remove gaps in the human sequence, and GERP++ scores were computed for\
every position with at least 3 ungapped species present.  Importantly, the human sequence was\
removed from the alignment and not included in either the neutral rate estimation or the\
site-specific "observed" estimates, and therefore is not included in the RS score.  This is\
consistent with the published work on GERP, and is done to eliminate the confounding influence of\
deleterious derived alleles segregating in the human population that are present in the reference\
sequence.  The phylogenetic tree used was the generally accepted topology.  Neutral branch lengths\
were estimated from 4-fold degenerate sites in the alignment. </p> \
\
<h2>Credits</h2> \
\
<p>The RS\
scores were generated by David Goode, Dept. of Genetics, Stanford University.  GERP++ was developed\
by Eugene Davydov and Serafim Batzoglou, Dept. of Computer Science, Stanford University; Arend\
Sidow, Depts. of Pathology and Genetics, Stanford University; and Gregory Cooper, HudsonAlpha\
Institute for Biotechnology, Huntsville, AL. </p> \
\
<h2>References</h2> \
<p>\
Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program, Green ED, Batzoglou S, Sidow\
A.\
<a href="https://genome.cshlp.org/content/15/7/901.long" target="_blank">\
Distribution and intensity of constraint in mammalian genomic sequence</a>.\
<em>Genome Res</em>. 2005 Jul;15(7):901-13.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15965027" target="_blank">15965027</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172034/" target="_blank">PMC1172034</a>\
</p>\
\
<p>\
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S.\
<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001025"\
target="_blank">Identifying a high fraction of the human genome to be under selective constraint\
using GERP++</a>. <em>PLoS Comput Biol</em>. 2010 Dec 2;6(12):e1001025.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21152010" target="_blank">21152010</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996323/" target="_blank">PMC2996323</a>\
</p>\
\
<p>For more information on using GERP to detect putatively functional genetic variation: </p>\
<p>\
Cooper GM, Goode DL, Ng SB, Sidow A, Bamshad MJ, Shendure J, Nickerson DA.\
<a href="https://www.nature.com/articles/nmeth0410-250" target="_blank">\
Single-nucleotide evolutionary constraint scores highlight disease-causing mutations</a>.\
<em>Nat Methods</em>. 2010 Apr;7(4):250-1.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20354513" target="_blank">20354513</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145250/" target="_blank">PMC3145250</a>\
</p>\
\
<p>\
Goode DL, Cooper GM, Schmutz J, Dickson M, Gonzales E, Tsai M, Karra K, Davydov E, Batzoglou S,\
Myers RM <em>et al</em>.\
<a href="https://genome.cshlp.org/content/20/3/301.long" target="_blank">\
Evolutionary constraint facilitates interpretation of genetic variation in resequenced human\
genomes</a>.\
<em>Genome Res</em>. 2010 Mar;20(3):301-10.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20067941" target="_blank">20067941</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2840986/" target="_blank">PMC2840986</a>\
</p>\
	compGeno	0	autoScale on\
group compGeno\
longLabel GERP scores for mammalian alignments\
maxHeightPixels 128:64:20\
priority 105\
shortLabel GERP\
track allMm9RS_BW\
type bigWig -10 5\
visibility hide\

wgEncodeLicrHistoneKidneyH3k4me1MAdult8wksC57bl6StdPk	Kidney H3K4m1	broadPeak	Kidney 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	105	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Kidney H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k4me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep1V2	LgInt Aln 1	bam	Large Intestine A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	105	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel LgInt Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=LGINT rep=rep1\
track wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep1V2\
type bam\

wgEncodeSydhTfbsMelMaxIggrabSig	MEL Max	bigWig 1.000000 120749.000000	MEL Max TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	105	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Max TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Max\
subGroups view=Signal factor=MAX cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelMaxIggrabSig\
type bigWig 1.000000 120749.000000\

wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep1	MEL PR 1	bigWig 1.000000 30018.000000	MEL Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	105	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel MEL PR 1\
subGroups view=PlusRawSignal age=IMMORTAL cellType=MEL localization=CELL rnaExtract=POLYA sex=M strain=UKN rep=rep1\
track wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep1\
type bigWig 1.000000 30018.000000\

wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep2	Gen Fat Pad H 2	broadPeak	Genital Fat Pad DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	106	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Genital Fat Pad DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Gen Fat Pad H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=GFAT sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseGfatC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneKidneyH3k4me1MAdult8wksC57bl6StdSig	Kidney H3K4m1	bigWig 0.130000 16.070000	Kidney 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	106	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Kidney H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k4me1MAdult8wksC57bl6StdSig\
type bigWig 0.130000 16.070000\
viewLimits 0.2:3\

wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep1	LgInt - 1	bigWig 1.000000 318236.000000	Large Intestine A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	106	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel LgInt - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LGINT rep=rep1\
track wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep1\
type bigWig 1.000000 318236.000000\

wgEncodeSydhTfbsMelMazab85725IggrabPk	MEL MAZ P	narrowPeak	MEL MAZ (ab85725) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	106	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL MAZ (ab85725) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL MAZ P\
subGroups view=Peaks factor=MAZAB85725 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelMazab85725IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep2	MEL PR 2	bigWig 1.000000 58514.000000	MEL Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	106	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig\
shortLabel MEL PR 2\
subGroups view=PlusRawSignal age=IMMORTAL cellType=MEL localization=CELL rnaExtract=POLYA sex=M strain=UKN rep=rep2\
track wgEncodeUwRnaSeqMelCellPolyaMImmortalUknPlusRawRep2\
type bigWig 1.000000 58514.000000\

wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep2	Gen Fat Pad P 2	narrowPeak	Genital Fat Pad DNaseI HS Peaks Rep 2 from ENCODE/UW	3	107	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Genital Fat Pad DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Gen Fat Pad P 2\
subGroups view=Peaks age=ADULT8WKS cellType=GFAT sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseGfatC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeLicrHistoneKidneyH3k4me3MAdult8wksC57bl6StdPk	Kidney H3K4m3	broadPeak	Kidney 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	107	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Kidney H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k4me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep1	LgInt + 1	bigWig 1.000000 708868.000000	Large Intestine A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	107	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel LgInt + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LGINT rep=rep1\
track wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep1\
type bigWig 1.000000 708868.000000\

wgEncodeSydhTfbsMelMazab85725IggrabSig	MEL MAZ S	bigWig 1.000000 455.000000	MEL MAZ (ab85725) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	107	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL MAZ (ab85725) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL MAZ S\
subGroups view=Signal factor=MAZAB85725 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelMazab85725IggrabSig\
type bigWig 1.000000 455.000000\

wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep1	MEL S 1	bigWig 1.000000 200174.000000	MEL Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW	2	107	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel MEL S 1\
subGroups view=Signal age=IMMORTAL cellType=MEL localization=CELL rnaExtract=POLYA sex=M strain=UKN rep=rep1\
track wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep1\
type bigWig 1.000000 200174.000000\

wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep2	Gen Fat Pad S 2	bigWig 1.000000 186127.000000	Genital Fat Pad DNaseI HS Signal Rep 2 from ENCODE/UW	2	108	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Genital Fat Pad DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Gen Fat Pad S 2\
subGroups view=Signal age=ADULT8WKS cellType=GFAT sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseGfatC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 186127.000000\

wgEncodeLicrHistoneKidneyH3k4me3MAdult8wksC57bl6StdSig	Kidney H3K4m3	bigWig 0.110000 57.959999	Kidney 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	108	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Kidney H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k4me3MAdult8wksC57bl6StdSig\
type bigWig 0.110000 57.959999\
viewLimits 0.2:10\

wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep2V2	LgInt Aln 2	bam	Large Intestine A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	108	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel LgInt Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=LGINT rep=rep2\
track wgEncodeCshlLongRnaSeqLgintAdult8wksAlnRep2V2\
type bam\

wgEncodeSydhTfbsMelMxi1af4185IggrabPk	MEL Mxi1	narrowPeak	MEL Mxi1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	108	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Mxi1 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL Mxi1\
subGroups view=Peaks factor=MXI1AF4185 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelMxi1af4185IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep2	MEL S 2	bigWig 1.000000 58534.000000	MEL Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW	2	108	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal\
shortLabel MEL S 2\
subGroups view=Signal age=IMMORTAL cellType=MEL localization=CELL rnaExtract=POLYA sex=M strain=UKN rep=rep2\
track wgEncodeUwRnaSeqMelCellPolyaMImmortalUknSigRep2\
type bigWig 1.000000 58534.000000\

wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep1	Headless Emb H 1	broadPeak	Headless Embryo DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	109	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel Headless Embryo DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Headless Emb H 1\
subGroups view=Hotspots age=E11HALF cellType=HEADLEMBRYO sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneKidneyH3k27acMAdult8wksC57bl6StdPk	Kidney H3K27a	broadPeak	Kidney 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	109	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Kidney H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep2	LgInt - 2	bigWig 1.000000 327311.000000	Large Intestine A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	109	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel LgInt - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LGINT rep=rep2\
track wgEncodeCshlLongRnaSeqLgintAdult8wksMinusRawRep2\
type bigWig 1.000000 327311.000000\

wgEncodeSydhTfbsMelMxi1af4185IggrabSig	MEL Mxi1	bigWig 1.000000 80915.000000	MEL Mxi1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	109	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Mxi1 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Mxi1\
subGroups view=Signal factor=MXI1AF4185 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelMxi1af4185IggrabSig\
type bigWig 1.000000 80915.000000\

wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep1	NIH-3T3 A 1	bam	NIH-3T3 Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW	0	109	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel NIH-3T3 Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel NIH-3T3 A 1\
subGroups view=Alignments age=IMMORTAL cellType=NIH3T3 localization=CELL rnaExtract=POLYA sex=M strain=NIHS rep=rep1\
track wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep1\
type bam\

wgEncodeUwDnaseHlembryoCd1ME11halfPkRep1	Headless Emb P 1	narrowPeak	Headless Embryo DNaseI HS Peaks Rep 1 from ENCODE/UW	3	110	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel Headless Embryo DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Headless Emb P 1\
subGroups view=Peaks age=E11HALF cellType=HEADLEMBRYO sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseHlembryoCd1ME11halfPkRep1\
type narrowPeak\

wgEncodeLicrHistoneKidneyH3k27acMAdult8wksC57bl6StdSig	Kidney H3K27a	bigWig 0.110000 37.259998	Kidney 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	110	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Kidney H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.110000 37.259998\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep2	LgInt + 2	bigWig 1.000000 1055697.000000	Large Intestine A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	110	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel LgInt + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LGINT rep=rep2\
track wgEncodeCshlLongRnaSeqLgintAdult8wksPlusRawRep2\
type bigWig 1.000000 1055697.000000\

wgEncodeSydhTfbsMelNelfeIggrabPk	MEL NELFe	narrowPeak	MEL NELFe TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	110	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL NELFe TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL NELFe\
subGroups view=Peaks factor=NELFE cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelNelfeIggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep2	NIH-3T3 A 2	bam	NIH-3T3 Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW	0	110	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel NIH-3T3 Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel NIH-3T3 A 2\
subGroups view=Alignments age=IMMORTAL cellType=NIH3T3 localization=CELL rnaExtract=POLYA sex=M strain=NIHS rep=rep2\
track wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsAlnRep2\
type bam\

wgEncodeUwDnaseHlembryoCd1ME11halfSigRep1	Headless Emb S 1	bigWig 1.000000 77111.000000	Headless Embryo DNaseI HS Signal Rep 1 from ENCODE/UW	2	111	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel Headless Embryo DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Headless Emb S 1\
subGroups view=Signal age=E11HALF cellType=HEADLEMBRYO sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseHlembryoCd1ME11halfSigRep1\
type bigWig 1.000000 77111.000000\

wgEncodeLicrHistoneKidneyH3k27me3MAdult8wksC57bl6StdPk	Kidney H3K27m3	broadPeak	Kidney 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	111	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Kidney H3K27m3\
subGroups view=Peaks age=A1DLT8W factor=H3K27ME3 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k27me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLgintAdult8wksContigs	LgInt C	bed 6 +	Large Intestine A8 Long RNA-seq Contigs from ENCODE/CSHL	3	111	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel LgInt C\
subGroups view=Contigs age=ADULT8WKS cellType=LGINT rep=repP\
track wgEncodeCshlLongRnaSeqLgintAdult8wksContigs\
type bed 6 +\

wgEncodeSydhTfbsMelNelfeIggrabSig	MEL NELFe	bigWig 1.000000 114421.000000	MEL NELFe TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	111	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL NELFe TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL NELFe\
subGroups view=Signal factor=NELFE cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelNelfeIggrabSig\
type bigWig 1.000000 114421.000000\

wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep1	NIH-3T3 MR 1	bigWig 1.000000 104138.000000	NIH-3T3 Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	111	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel NIH-3T3 MR 1\
subGroups view=MinusRawSignal age=IMMORTAL cellType=NIH3T3 localization=CELL rnaExtract=POLYA sex=M strain=NIHS rep=rep1\
track wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep1\
type bigWig 1.000000 104138.000000\

wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep2	Headless Emb H 2	broadPeak	Headless Embryo DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	112	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel Headless Embryo DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Headless Emb H 2\
subGroups view=Hotspots age=E11HALF cellType=HEADLEMBRYO sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseHlembryoCd1ME11halfHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneKidneyH3k27me3MAdult8wksC57bl6StdSig	Kidney H3K27m3	bigWig 0.110000 43.450001	Kidney 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	112	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Kidney H3K27m3\
subGroups view=Signal age=A1DLT8W factor=H3K27ME3 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k27me3MAdult8wksC57bl6StdSig\
type bigWig 0.110000 43.450001\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqLgintAdult8wksJunctions	LgInt J	bed 6 +	Large Intestine A8 Long RNA-seq Junctions from ENCODE/CSHL	0	112	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel LgInt J\
subGroups view=SJunctions age=ADULT8WKS cellType=LGINT rep=repP\
track wgEncodeCshlLongRnaSeqLgintAdult8wksJunctions\
type bed 6 +\

wgEncodeSydhTfbsMelNrf2IggrabPk	MEL Nrf2 P	narrowPeak	MEL Nrf2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	112	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Nrf2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL Nrf2 P\
subGroups view=Peaks factor=NRF2 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelNrf2IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep2	NIH-3T3 MR 2	bigWig 1.000000 99501.000000	NIH-3T3 Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	112	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel NIH-3T3 MR 2\
subGroups view=MinusRawSignal age=IMMORTAL cellType=NIH3T3 localization=CELL rnaExtract=POLYA sex=M strain=NIHS rep=rep2\
track wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsMinusRawRep2\
type bigWig 1.000000 99501.000000\

wgEncodeUwDnaseHlembryoCd1ME11halfPkRep2	Headless Emb P 2	narrowPeak	Headless Embryo DNaseI HS Peaks Rep 2 from ENCODE/UW	3	113	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel Headless Embryo DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Headless Emb P 2\
subGroups view=Peaks age=E11HALF cellType=HEADLEMBRYO sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseHlembryoCd1ME11halfPkRep2\
type narrowPeak\

wgEncodeLicrHistoneKidneyH3k36me3MAdult8wksC57bl6StdPk	Kidney H3K36m3	broadPeak	Kidney 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	113	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Kidney H3K36m3\
subGroups view=Peaks age=A1DLT8W factor=H3K36ME3 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k36me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLimbE14halfAlnRep1	Limb Aln 1	bam	Limb E14.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	113	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb E14.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Limb Aln 1\
subGroups view=Alignments age=E14HALF cellType=LIMB rep=rep1\
track wgEncodeCshlLongRnaSeqLimbE14halfAlnRep1\
type bam\

wgEncodeSydhTfbsMelNrf2IggrabSig	MEL Nrf2 S	bigWig 1.000000 400.000000	MEL Nrf2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	113	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Nrf2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Nrf2 S\
subGroups view=Signal factor=NRF2 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelNrf2IggrabSig\
type bigWig 1.000000 400.000000\

wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep1	NIH-3T3 PR 1	bigWig 1.000000 56693.000000	NIH-3T3 Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	113	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel NIH-3T3 PR 1\
subGroups view=PlusRawSignal age=IMMORTAL cellType=NIH3T3 localization=CELL rnaExtract=POLYA sex=M strain=NIHS rep=rep1\
track wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep1\
type bigWig 1.000000 56693.000000\

wgEncodeUwDnaseHlembryoCd1ME11halfSigRep2	Headless Emb S 2	bigWig 1.000000 58832.000000	Headless Embryo DNaseI HS Signal Rep 2 from ENCODE/UW	2	114	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel Headless Embryo DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Headless Emb S 2\
subGroups view=Signal age=E11HALF cellType=HEADLEMBRYO sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseHlembryoCd1ME11halfSigRep2\
type bigWig 1.000000 58832.000000\

wgEncodeLicrHistoneKidneyH3k36me3MAdult8wksC57bl6StdSig	Kidney H3K36m3	bigWig 0.110000 24.240000	Kidney 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	114	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Kidney H3K36m3\
subGroups view=Signal age=A1DLT8W factor=H3K36ME3 cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyH3k36me3MAdult8wksC57bl6StdSig\
type bigWig 0.110000 24.240000\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep1	Limb - 1	bigWig 1.000000 317417.000000	Limb E14.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	114	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb E14.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Limb - 1\
subGroups view=MinusRawSignal age=E14HALF cellType=LIMB rep=rep1\
track wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep1\
type bigWig 1.000000 317417.000000\

wgEncodeSydhTfbsMelP300IggrabPkV2	MEL p300	narrowPeak	MEL p300 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	114	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL p300 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL p300\
subGroups view=Peaks factor=P300 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelP300IggrabPkV2\
type narrowPeak\

wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep2	NIH-3T3 PR 2	bigWig 1.000000 53523.000000	NIH-3T3 Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	114	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel NIH-3T3 PR 2\
subGroups view=PlusRawSignal age=IMMORTAL cellType=NIH3T3 localization=CELL rnaExtract=POLYA sex=M strain=NIHS rep=rep2\
track wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsPlusRawRep2\
type bigWig 1.000000 53523.000000\

wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep1	Heart H 1	broadPeak	Heart DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	115	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Heart H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=HEART sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneKidneyInputMAdult8wksC57bl6StdSig	Kidney Input	bigWig 0.140000 51.650002	Kidney 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	115	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Kidney Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=KIDNEY control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneKidneyInputMAdult8wksC57bl6StdSig\
type bigWig 0.140000 51.650002\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep1	Limb + 1	bigWig 1.000000 717738.000000	Limb E14.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	115	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb E14.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Limb + 1\
subGroups view=PlusRawSignal age=E14HALF cellType=LIMB rep=rep1\
track wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep1\
type bigWig 1.000000 717738.000000\

wgEncodeSydhTfbsMelP300IggrabSigV2	MEL p300	bigWig 1.000000 92232.000000	MEL p300 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	115	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL p300 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL p300\
subGroups view=Signal factor=P300 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelP300IggrabSigV2\
type bigWig 1.000000 92232.000000\

wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep1	NIH-3T3 S 1	bigWig 1.000000 104138.000000	NIH-3T3 Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW	2	115	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel NIH-3T3 S 1\
subGroups view=Signal age=IMMORTAL cellType=NIH3T3 localization=CELL rnaExtract=POLYA sex=M strain=NIHS rep=rep1\
track wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep1\
type bigWig 1.000000 104138.000000\

wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep1	Heart P 1	narrowPeak	Heart DNaseI HS Peaks Rep 1 from ENCODE/UW	3	116	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Heart P 1\
subGroups view=Peaks age=ADULT8WKS cellType=HEART sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqLimbE14halfAlnRep2	Limb Aln 2	bam	Limb E14.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	116	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb E14.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Limb Aln 2\
subGroups view=Alignments age=E14HALF cellType=LIMB rep=rep2\
track wgEncodeCshlLongRnaSeqLimbE14halfAlnRep2\
type bam\

wgEncodeLicrHistoneLimbH3k04me1UE14halfC57bl6StdPk	Limb H3K4m1	broadPeak	Limb E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	116	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Limb H3K4m1\
subGroups view=Peaks age=E14HALF factor=H3K04ME1 cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLimbH3k04me1UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsMelP300sc584IggrabPk	MEL p300 SC-584	narrowPeak	MEL p300 (SC-584) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	116	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL p300 (SC-584) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks\
shortLabel MEL p300 SC-584\
subGroups view=Peaks factor=P300SC584 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelP300sc584IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep2	NIH-3T3 S 2	bigWig 1.000000 99503.000000	NIH-3T3 Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW	2	116	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel NIH-3T3 S 2\
subGroups view=Signal age=IMMORTAL cellType=NIH3T3 localization=CELL rnaExtract=POLYA sex=M strain=NIHS rep=rep2\
track wgEncodeUwRnaSeqNih3t3CellPolyaMImmortalNihsSigRep2\
type bigWig 1.000000 99503.000000\

wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep1	Heart S 1	bigWig 1.000000 35686.000000	Heart DNaseI HS Signal Rep 1 from ENCODE/UW	2	117	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Heart S 1\
subGroups view=Signal age=ADULT8WKS cellType=HEART sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 35686.000000\

wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep2	Limb - 2	bigWig 1.000000 280410.000000	Limb E14.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	117	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb E14.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Limb - 2\
subGroups view=MinusRawSignal age=E14HALF cellType=LIMB rep=rep2\
track wgEncodeCshlLongRnaSeqLimbE14halfMinusRawRep2\
type bigWig 1.000000 280410.000000\

wgEncodeLicrHistoneLimbH3k04me1UE14halfC57bl6StdSig	Limb H3K4m1	bigWig 0.130000 25.370001	Limb E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	117	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Limb H3K4m1\
subGroups view=Signal age=E14HALF factor=H3K04ME1 cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLimbH3k04me1UE14halfC57bl6StdSig\
type bigWig 0.130000 25.370001\
viewLimits 0.2:3\

wgEncodeSydhTfbsMelP300sc584IggrabSig	MEL p300 SC-584	bigWig 1.000000 93877.000000	MEL p300 (SC-584) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	117	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL p300 (SC-584) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig\
shortLabel MEL p300 SC-584\
subGroups view=Signal factor=P300SC584 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelP300sc584IggrabSig\
type bigWig 1.000000 93877.000000\

wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep1	Patski A 1	bam	Patski Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW	0	117	204	121	141	229	188	198	0	0	0				regulation	1	color 204,121,1677\
longLabel Patski Immortal Cells RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Patski A 1\
subGroups view=Alignments age=IMMORTAL cellType=PATSKI localization=CELL rnaExtract=POLYA sex=F strain=SPBL6 rep=rep1\
track wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep1\
type bam\

wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep2	Heart H 2	broadPeak	Heart DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	118	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Heart H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=HEART sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseHeartC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep2	Limb + 2	bigWig 1.000000 697216.000000	Limb E14.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	118	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb E14.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Limb + 2\
subGroups view=PlusRawSignal age=E14HALF cellType=LIMB rep=rep2\
track wgEncodeCshlLongRnaSeqLimbE14halfPlusRawRep2\
type bigWig 1.000000 697216.000000\

wgEncodeLicrHistoneLimbH3k04me3UE14halfC57bl6StdPk	Limb H3K4m3	broadPeak	Limb E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	118	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Limb H3K4m3\
subGroups view=Peaks age=E14HALF factor=H3K04ME3 cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLimbH3k04me3UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsMelPol2Dm2p5dIggrabPk	MEL Pol2 D	narrowPeak	MEL Pol2 DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	118	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Pol2 DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL Pol2 D\
subGroups view=Peaks factor=POL2 cellType=MEL control=IGGRAB treatment=DM2P5D\
track wgEncodeSydhTfbsMelPol2Dm2p5dIggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep2	Patski A 2	bam	Patski Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW	0	118	204	121	141	229	188	198	0	0	0				regulation	1	color 204,121,1677\
longLabel Patski Immortal Cells RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Patski A 2\
subGroups view=Alignments age=IMMORTAL cellType=PATSKI localization=CELL rnaExtract=POLYA sex=F strain=SPBL6 rep=rep2\
track wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6AlnRep2\
type bam\

wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep2	Heart P 2	narrowPeak	Heart DNaseI HS Peaks Rep 2 from ENCODE/UW	3	119	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Heart DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Heart P 2\
subGroups view=Peaks age=ADULT8WKS cellType=HEART sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseHeartC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqLimbE14halfContigs	Limb C	bed 6 +	Limb E14.5 Long RNA-seq Contigs from ENCODE/CSHL	3	119	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb E14.5 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Limb C\
subGroups view=Contigs age=E14HALF cellType=LIMB rep=repP\
track wgEncodeCshlLongRnaSeqLimbE14halfContigs\
type bed 6 +\

wgEncodeLicrHistoneLimbH3k04me3UE14halfC57bl6StdSig	Limb H3K4m3	bigWig 0.130000 47.400002	Limb E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	119	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Limb H3K4m3\
subGroups view=Signal age=E14HALF factor=H3K04ME3 cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLimbH3k04me3UE14halfC57bl6StdSig\
type bigWig 0.130000 47.400002\
viewLimits 0.2:10\

wgEncodeSydhTfbsMelPol2Dm2p5dIggrabSig	MEL Pol2 D	bigWig 1.000000 40837.000000	MEL Pol2 DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	119	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Pol2 DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Pol2 D\
subGroups view=Signal factor=POL2 cellType=MEL control=IGGRAB treatment=DM2P5D\
track wgEncodeSydhTfbsMelPol2Dm2p5dIggrabSig\
type bigWig 1.000000 40837.000000\

wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep1	Patski MR 1	bigWig 1.000000 223741.000000	Patski Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	119	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Patski Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Patski MR 1\
subGroups view=MinusRawSignal age=IMMORTAL cellType=PATSKI localization=CELL rnaExtract=POLYA sex=F strain=SPBL6 rep=rep1\
track wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep1\
type bigWig 1.000000 223741.000000\

wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep2	Heart S 2	bigWig 1.000000 65466.000000	Heart DNaseI HS Signal Rep 2 from ENCODE/UW	2	120	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Heart DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Heart S 2\
subGroups view=Signal age=ADULT8WKS cellType=HEART sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseHeartC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 65466.000000\

wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdPk	Limb H3K27a	broadPeak	Limb E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	120	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Limb H3K27a\
subGroups view=Peaks age=E14HALF factor=H3K27AC cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLimbE14halfJunctions	Limb J	bed 6 +	Limb E14.5 Long RNA-seq Junctions from ENCODE/CSHL	0	120	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Limb E14.5 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Limb J\
subGroups view=SJunctions age=E14HALF cellType=LIMB rep=repP\
track wgEncodeCshlLongRnaSeqLimbE14halfJunctions\
type bed 6 +\

wgEncodeSydhTfbsMelPol2IggmusPk	MEL Pol2	narrowPeak	MEL Pol2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	120	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Pol2 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks\
shortLabel MEL Pol2\
subGroups view=Peaks factor=POL2 cellType=MEL control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsMelPol2IggmusPk\
type narrowPeak\

wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep2	Patski MR 2	bigWig 1.000000 74671.000000	Patski Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	120	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Patski Immortal Cells RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Patski MR 2\
subGroups view=MinusRawSignal age=IMMORTAL cellType=PATSKI localization=CELL rnaExtract=POLYA sex=F strain=SPBL6 rep=rep2\
track wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6MinusRawRep2\
type bigWig 1.000000 74671.000000\

wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep1	Hind Limb Bud H 1	broadPeak	Hind Limb Bud DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	121	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Hind Limb Bud DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Hind Limb Bud H 1\
subGroups view=Hotspots age=E11HALF cellType=HLBUD sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdSig	Limb H3K27a	bigWig 0.120000 48.669998	Limb E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	121	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Limb H3K27a\
subGroups view=Signal age=E14HALF factor=H3K27AC cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLimbH3k27acUE14halfC57bl6StdSig\
type bigWig 0.120000 48.669998\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep1V2	Liver A8 Aln 1	bam	Liver A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	121	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Liver A8 Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep1V2\
type bam\

wgEncodeSydhTfbsMelPol2IggmusSig	MEL Pol2	bigWig 1 13695	MEL Pol2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	121	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Pol2 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig\
shortLabel MEL Pol2\
subGroups view=Signal factor=POL2 cellType=MEL control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsMelPol2IggmusSig\
type bigWig 1 13695\

wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep1	Patski PR 1	bigWig 1.000000 471388.000000	Patski Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	121	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Patski Immortal Cells RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Patski PR 1\
subGroups view=PlusRawSignal age=IMMORTAL cellType=PATSKI localization=CELL rnaExtract=POLYA sex=F strain=SPBL6 rep=rep1\
track wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep1\
type bigWig 1.000000 471388.000000\

wgEncodeUwDnaseHlbudCd1ME11halfPkRep1	Hind Limb Bud P 1	narrowPeak	Hind Limb Bud DNaseI HS Peaks Rep 1 from ENCODE/UW	3	122	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Hind Limb Bud DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Hind Limb Bud P 1\
subGroups view=Peaks age=E11HALF cellType=HLBUD sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseHlbudCd1ME11halfPkRep1\
type narrowPeak\

wgEncodeLicrHistoneLimbInputUE14halfC57bl6StdSig	Limb Input	bigWig 0.150000 46.419998	Limb E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	122	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Limb E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Limb Input\
subGroups view=Signal age=E14HALF factor=INPUT cellType=LIMB control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLimbInputUE14halfC57bl6StdSig\
type bigWig 0.150000 46.419998\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep1	Liver A8 - 1	bigWig 1.000000 547737.000000	Liver A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	122	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Liver A8 - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep1\
type bigWig 1.000000 547737.000000\

wgEncodeSydhTfbsMelPol2s2IggrabPk	MEL Pol2S2	narrowPeak	MEL Pol2(phosphoS2) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	122	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Pol2(phosphoS2) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL Pol2S2\
subGroups view=Peaks factor=POL2S2 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelPol2s2IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep2	Patski PR 2	bigWig 1.000000 48875.000000	Patski Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	122	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Patski Immortal Cells RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Patski PR 2\
subGroups view=PlusRawSignal age=IMMORTAL cellType=PATSKI localization=CELL rnaExtract=POLYA sex=F strain=SPBL6 rep=rep2\
track wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6PlusRawRep2\
type bigWig 1.000000 48875.000000\

wgEncodeUwDnaseHlbudCd1ME11halfSigRep1	Hind Limb Bud S 1	bigWig 1.000000 62621.000000	Hind Limb Bud DNaseI HS Signal Rep 1 from ENCODE/UW	2	123	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Hind Limb Bud DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Hind Limb Bud S 1\
subGroups view=Signal age=E11HALF cellType=HLBUD sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseHlbudCd1ME11halfSigRep1\
type bigWig 1.000000 62621.000000\

wgEncodeLicrHistoneLiverH3k4me1MAdult8wksC57bl6StdPk	Liver 8w H3K4m1	broadPeak	Liver 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	123	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 8w H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k4me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep1	Liver A8 + 1	bigWig 1.000000 1395240.000000	Liver A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	123	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Liver A8 + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep1\
type bigWig 1.000000 1395240.000000\

wgEncodeSydhTfbsMelPol2s2IggrabSig	MEL Pol2S2	bigWig 1.000000 44277.000000	MEL Pol2(phosphoS2) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	123	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Pol2(phosphoS2) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Pol2S2\
subGroups view=Signal factor=POL2S2 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelPol2s2IggrabSig\
type bigWig 1.000000 44277.000000\

wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep1	Patski S 1	bigWig 1.000000 471388.000000	Patski Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW	2	123	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Patski Immortal Cells RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Patski S 1\
subGroups view=Signal age=IMMORTAL cellType=PATSKI localization=CELL rnaExtract=POLYA sex=F strain=SPBL6 rep=rep1\
track wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep1\
type bigWig 1.000000 471388.000000\

wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep2	Hind Limb Bud H 2	broadPeak	Hind Limb Bud DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	124	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Hind Limb Bud DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Hind Limb Bud H 2\
subGroups view=Hotspots age=E11HALF cellType=HLBUD sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseHlbudCd1ME11halfHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneLiverH3k04me1UE14halfC57bl6StdPk	Liver 14.5 H3K4m1	broadPeak	Liver E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	124	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 14.5 H3K4m1\
subGroups view=Peaks age=E14HALF factor=H3K04ME1 cellType=LIVER control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k04me1UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep2V2	Liver A8 Aln 2	bam	Liver A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	124	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Liver A8 Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverAdult8wksAlnRep2V2\
type bam\

wgEncodeSydhTfbsMelRad21Dm2p5dIggrabPk	MEL Rad21 D	narrowPeak	MEL Rad21 DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	124	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Rad21 DMSO 2% TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL Rad21 D\
subGroups view=Peaks factor=RAD21 cellType=MEL control=IGGRAB treatment=DM2P5D\
track wgEncodeSydhTfbsMelRad21Dm2p5dIggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep2	Patski S 2	bigWig 1.000000 74671.000000	Patski Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW	2	124	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Patski Immortal Cells RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Patski S 2\
subGroups view=Signal age=IMMORTAL cellType=PATSKI localization=CELL rnaExtract=POLYA sex=F strain=SPBL6 rep=rep2\
track wgEncodeUwRnaSeqPatskiCellPolyaFImmortalSpbl6SigRep2\
type bigWig 1.000000 74671.000000\

wgEncodeUwDnaseHlbudCd1ME11halfPkRep2	Hind Limb Bud P 2	narrowPeak	Hind Limb Bud DNaseI HS Peaks Rep 2 from ENCODE/UW	3	125	102	50	200	178	152	227	0	0	0				regulation	1	color 102,50,200\
longLabel Hind Limb Bud DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Hind Limb Bud P 2\
subGroups view=Peaks age=E11HALF cellType=HLBUD sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseHlbudCd1ME11halfPkRep2\
type narrowPeak\

wgEncodeLicrHistoneLiverH3k4me1MAdult8wksC57bl6StdSig	Liver 8w H3K4m1	bigWig 0.140000 31.250000	Liver 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	125	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 8w H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k4me1MAdult8wksC57bl6StdSig\
type bigWig 0.140000 31.250000\
viewLimits 0.2:3\

wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep2	Liver A8 - 2	bigWig 1.000000 513460.000000	Liver A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	125	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Liver A8 - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverAdult8wksMinusRawRep2\
type bigWig 1.000000 513460.000000\

wgEncodeSydhTfbsMelRad21Dm2p5dIggrabSig	MEL Rad21 D	bigWig 1.000000 64232.000000	MEL Rad21 DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	125	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Rad21 DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Rad21 D\
subGroups view=Signal factor=RAD21 cellType=MEL control=IGGRAB treatment=DM2P5D\
track wgEncodeSydhTfbsMelRad21Dm2p5dIggrabSig\
type bigWig 1.000000 64232.000000\

wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep1	SkMuscle 8w A 1	bam	Skeletal Muscle Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	125	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel Skeletal Muscle Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel SkMuscle 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=SKMUSCLE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDnaseHlbudCd1ME11halfSigRep2	Hind Limb Bud S 2	bigWig 1.000000 144814.000000	Hind Limb Bud DNaseI HS Signal Rep 2 from ENCODE/UW	2	126	102	50	200	178	152	227	0	0	0				regulation	0	color 102,50,200\
longLabel Hind Limb Bud DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Hind Limb Bud S 2\
subGroups view=Signal age=E11HALF cellType=HLBUD sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseHlbudCd1ME11halfSigRep2\
type bigWig 1.000000 144814.000000\

wgEncodeLicrHistoneLiverH3k04me1UE14halfC57bl6StdSig	Liver 14.5 H3K4m1	bigWig 0.120000 12.900000	Liver E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	126	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 14.5 H3K4m1\
subGroups view=Signal age=E14HALF factor=H3K04ME1 cellType=LIVER control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k04me1UE14halfC57bl6StdSig\
type bigWig 0.120000 12.900000\
viewLimits 0.2:3\

wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep2	Liver A8 + 2	bigWig 1.000000 2117547.000000	Liver A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	126	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Liver A8 + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverAdult8wksPlusRawRep2\
type bigWig 1.000000 2117547.000000\

wgEncodeSydhTfbsMelRad21IggrabPk	MEL Rad21	narrowPeak	MEL Rad21 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	126	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL Rad21 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL Rad21\
subGroups view=Peaks factor=RAD21 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelRad21IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep2	SkMuscle 8w A 2	bam	Skeletal Muscle Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW	0	126	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel Skeletal Muscle Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel SkMuscle 8w A 2\
subGroups view=Alignments age=ADULT8WKS cellType=SKMUSCLE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep1	Kidney H 1	broadPeak	Kidney DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	127	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Kidney H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=KIDNEY sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdPk	Liver 8w H3K4m3	broadPeak	Liver 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	127	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 8w H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverAdult8wksContigs	Liver A8 C	bed 6 +	Liver A8 Long RNA-seq Contigs from ENCODE/CSHL	3	127	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Liver A8 C\
subGroups view=Contigs age=ADULT8WKS cellType=LIVER rep=repP\
track wgEncodeCshlLongRnaSeqLiverAdult8wksContigs\
type bed 6 +\

wgEncodeSydhTfbsMelRad21IggrabSig	MEL Rad21	bigWig 1.000000 79946.000000	MEL Rad21 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	127	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Rad21 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Rad21\
subGroups view=Signal factor=RAD21 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelRad21IggrabSig\
type bigWig 1.000000 79946.000000\

wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep1	SkMuscle 8w MR 1	bigWig 1.000000 161096.000000	Skeletal Muscle Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	127	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel Skeletal Muscle Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel SkMuscle 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=SKMUSCLE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 161096.000000\

wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep1	Kidney P 1	narrowPeak	Kidney DNaseI HS Peaks Rep 1 from ENCODE/UW	3	128	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Kidney P 1\
subGroups view=Peaks age=ADULT8WKS cellType=KIDNEY sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeLicrHistoneLiverH3k04me3UE14halfC57bl6StdPk	Liver 14.5 H3K4m3	broadPeak	Liver E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	128	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 14.5 H3K4m3\
subGroups view=Peaks age=E14HALF factor=H3K04ME3 cellType=LIVER control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k04me3UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverAdult8wksJunctions	Liver A8 J	bed 6 +	Liver A8 Long RNA-seq Junctions from ENCODE/CSHL	0	128	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Liver A8 J\
subGroups view=SJunctions age=ADULT8WKS cellType=LIVER rep=repP\
track wgEncodeCshlLongRnaSeqLiverAdult8wksJunctions\
type bed 6 +\

wgEncodeSydhTfbsMelSin3anb6001263IggrabPk	MEL SIN3A_N	narrowPeak	MEL SIN3A (NB600-1263) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	128	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL SIN3A (NB600-1263) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL SIN3A_N\
subGroups view=Peaks factor=SIN3ANB6001263 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelSin3anb6001263IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep2	SkMuscle 8w MR 2	bigWig 1.000000 244245.000000	Skeletal Muscle Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	128	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel Skeletal Muscle Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel SkMuscle 8w MR 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=SKMUSCLE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6MinusRawRep2\
type bigWig 1.000000 244245.000000\

wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep1	Kidney S 1	bigWig 1.000000 74651.000000	Kidney DNaseI HS Signal Rep 1 from ENCODE/UW	2	129	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Kidney S 1\
subGroups view=Signal age=ADULT8WKS cellType=KIDNEY sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 74651.000000\

wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdSig	Liver 8w H3K4m3	bigWig 0.140000 72.970001	Liver 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	129	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 8w H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k4me3MAdult8wksC57bl6StdSig\
type bigWig 0.140000 72.970001\
viewLimits 0.2:10\

wgEncodeCshlLongRnaSeqLiverE14AlnRep1	Liver E14 Aln 1	bam	Liver E14 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	129	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Liver E14 Aln 1\
subGroups view=Alignments age=E14 cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverE14AlnRep1\
type bam\

wgEncodeSydhTfbsMelSin3anb6001263IggrabSig	MEL SIN3A_N	bigWig 1.000000 86536.000000	MEL SIN3A (NB600-1263) IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	129	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL SIN3A (NB600-1263) IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL SIN3A_N\
subGroups view=Signal factor=SIN3ANB6001263 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelSin3anb6001263IggrabSig\
type bigWig 1.000000 86536.000000\

wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep1	SkMuscle 8w PR 1	bigWig 1.000000 161056.000000	Skeletal Muscle Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	129	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel Skeletal Muscle Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel SkMuscle 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=SKMUSCLE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 161056.000000\

wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep2	Kidney H 2	broadPeak	Kidney DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	130	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Kidney H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=KIDNEY sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseKidneyC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneLiverH3k04me3UE14halfC57bl6StdSig	Liver 14.5 H3K4m3	bigWig 0.140000 58.919998	Liver E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	130	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 14.5 H3K4m3\
subGroups view=Signal age=E14HALF factor=H3K04ME3 cellType=LIVER control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k04me3UE14halfC57bl6StdSig\
type bigWig 0.140000 58.919998\
viewLimits 0.2:10\

wgEncodeCshlLongRnaSeqLiverE14MinusRawRep1	Liver E14 - 1	bigWig 1.000000 14241027.000000	Liver E14 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	130	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Liver E14 - 1\
subGroups view=MinusRawSignal age=E14 cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverE14MinusRawRep1\
type bigWig 1.000000 14241027.000000\

wgEncodeSydhTfbsMelSmc3ab9263IggrabPk	MEL SMC3	narrowPeak	MEL SMC3 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	130	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL SMC3 TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL SMC3\
subGroups view=Peaks factor=SMC3ab9263 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelSmc3ab9263IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep2	SkMuscle 8w PR 2	bigWig 1.000000 244287.000000	Skeletal Muscle Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	130	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel Skeletal Muscle Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel SkMuscle 8w PR 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=SKMUSCLE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6PlusRawRep2\
type bigWig 1.000000 244287.000000\

wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep2	Kidney P 2	narrowPeak	Kidney DNaseI HS Peaks Rep 2 from ENCODE/UW	3	131	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Kidney DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Kidney P 2\
subGroups view=Peaks age=ADULT8WKS cellType=KIDNEY sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseKidneyC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeLicrHistoneLiverH3k09acMAdult8wksC57bl6StdPk	Liver 8w H3K9a	broadPeak	Liver 8w H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	131	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 8w H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 8w H3K9a\
subGroups view=Peaks age=A1DLT8W factor=H3K09AC cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k09acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverE14PlusRawRep1	Liver E14 + 1	bigWig 1.000000 15383945.000000	Liver E14 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	131	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Liver E14 + 1\
subGroups view=PlusRawSignal age=E14 cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverE14PlusRawRep1\
type bigWig 1.000000 15383945.000000\

wgEncodeSydhTfbsMelSmc3ab9263IggrabSig	MEL SMC3	bigWig 1.000000 102412.000000	MEL SMC3 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	131	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL SMC3 TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL SMC3\
subGroups view=Signal factor=SMC3ab9263 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelSmc3ab9263IggrabSig\
type bigWig 1.000000 102412.000000\

wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep1	SkMuscle 8w S 1	bigWig 1.000000 161097.000000	Skeletal Muscle Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	131	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel Skeletal Muscle Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel SkMuscle 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=SKMUSCLE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 161097.000000\

wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep2	Kidney S 2	bigWig 1.000000 39287.000000	Kidney DNaseI HS Signal Rep 2 from ENCODE/UW	2	132	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Kidney DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Kidney S 2\
subGroups view=Signal age=ADULT8WKS cellType=KIDNEY sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseKidneyC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 39287.000000\

wgEncodeLicrHistoneLiverH3k09acMAdult8wksC57bl6StdSig	Liver 8w H3K9a	bigWig 0.110000 42.980000	Liver 8w H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	132	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 8w H3K9a\
subGroups view=Signal age=A1DLT8W factor=H3K09AC cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k09acMAdult8wksC57bl6StdSig\
type bigWig 0.110000 42.980000\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqLiverE14AlnRep2	Liver E14 Aln 2	bam	Liver E14 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	132	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Liver E14 Aln 2\
subGroups view=Alignments age=E14 cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverE14AlnRep2\
type bam\

wgEncodeSydhTfbsMelTbpIggmusPk	MEL TBP	narrowPeak	MEL TBP TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	132	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL TBP TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL TBP\
subGroups view=Peaks factor=TBP cellType=MEL control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsMelTbpIggmusPk\
type narrowPeak\

wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep2	SkMuscle 8w S 2	bigWig 1.000000 244287.000000	Skeletal Muscle Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW	2	132	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel Skeletal Muscle Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel SkMuscle 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=SKMUSCLE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqSkmuscleCellPolyaMAdult8wksC57bl6SigRep2\
type bigWig 1.000000 244287.000000\

wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep1	Lg Intestine H 1	broadPeak	Large Intestine DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	133	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Lg Intestine H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=LGINT sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneLiverH3k27acMAdult8wksC57bl6StdPk	Liver 8w H3K27a	broadPeak	Liver 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	133	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 8w H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverE14MinusRawRep2	Liver E14 - 2	bigWig 1.000000 19676648.000000	Liver E14 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	133	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Liver E14 - 2\
subGroups view=MinusRawSignal age=E14 cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverE14MinusRawRep2\
type bigWig 1.000000 19676648.000000\

wgEncodeSydhTfbsMelTbpIggmusSig	MEL TBP	bigWig 1 60278	MEL TBP TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	133	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL TBP TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL TBP\
subGroups view=Signal factor=TBP cellType=MEL control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsMelTbpIggmusSig\
type bigWig 1 60278\

wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6AlnRep1	Spleen 8w A 1	bam	Spleen Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	133	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Spleen 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=SPLEEN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep1	Lg Intestine P 1	narrowPeak	Large Intestine DNaseI HS Peaks Rep 1 from ENCODE/UW	3	134	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Lg Intestine P 1\
subGroups view=Peaks age=ADULT8WKS cellType=LGINT sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeLicrHistoneLiverH3k27acUE14halfC57bl6StdPk	Liver 14.5 H3K27a	broadPeak	Liver E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	134	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 14.5 H3K27a\
subGroups view=Peaks age=E14HALF factor=H3K27AC cellType=LIVER control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k27acUE14halfC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverE14PlusRawRep2	Liver E14 + 2	bigWig 1.000000 18756232.000000	Liver E14 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	134	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Liver E14 + 2\
subGroups view=PlusRawSignal age=E14 cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverE14PlusRawRep2\
type bigWig 1.000000 18756232.000000\

wgEncodeSydhTfbsMelUbfsc13125IggmusPk	MEL UBF P	narrowPeak	MEL UBF (sc-13125) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	134	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL UBF (sc-13125) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL UBF P\
subGroups view=Peaks factor=UBFSC13125 cellType=MEL control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsMelUbfsc13125IggmusPk\
type narrowPeak\

wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6MinusRawRep1	Spleen 8w MR 1	bigWig 1.000000 123819.000000	Spleen Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	134	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Spleen 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=SPLEEN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 123819.000000\

wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep1	Lg Intestine S 1	bigWig 1.000000 48916.000000	Large Intestine DNaseI HS Signal Rep 1 from ENCODE/UW	2	135	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Lg Intestine S 1\
subGroups view=Signal age=ADULT8WKS cellType=LGINT sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 48916.000000\

wgEncodeLicrHistoneLiverH3k27acMAdult8wksC57bl6StdSig	Liver 8w H3K27a	bigWig 0.140000 42.110001	Liver 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	135	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 8w H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.140000 42.110001\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqLiverE14Contigs	Liver E14 C	bed 6 +	Liver E14 Long RNA-seq Contigs from ENCODE/CSHL	3	135	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Liver E14 C\
subGroups view=Contigs age=E14 cellType=LIVER rep=repP\
track wgEncodeCshlLongRnaSeqLiverE14Contigs\
type bed 6 +\

wgEncodeSydhTfbsMelUbfsc13125IggmusSig	MEL UBF S	bigWig 1.000000 384.000000	MEL UBF (sc-13125) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	135	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL UBF (sc-13125) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL UBF S\
subGroups view=Signal factor=UBFSC13125 cellType=MEL control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsMelUbfsc13125IggmusSig\
type bigWig 1.000000 384.000000\

wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6PlusRawRep1	Spleen 8w PR 1	bigWig 1.000000 373038.000000	Spleen Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	135	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Spleen 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=SPLEEN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 373038.000000\

wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep2	Lg Intestine H 2	broadPeak	Large Intestine DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	136	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Lg Intestine H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=LGINT sex=M strain=C57BL6 treatment=zNONE rep=rep2\
track wgEncodeUwDnaseLgintC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneLiverH3k27acUE14halfC57bl6StdSig	Liver 14.5 H3K27a	bigWig 0.100000 59.410000	Liver E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	136	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 14.5 H3K27a\
subGroups view=Signal age=E14HALF factor=H3K27AC cellType=LIVER control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k27acUE14halfC57bl6StdSig\
type bigWig 0.100000 59.410000\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqLiverE14Junctions	Liver E14 J	bed 6 +	Liver E14 Long RNA-seq Junctions from ENCODE/CSHL	0	136	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Liver E14 J\
subGroups view=SJunctions age=E14 cellType=LIVER rep=repP\
track wgEncodeCshlLongRnaSeqLiverE14Junctions\
type bed 6 +\

wgEncodeSydhTfbsMelUsf2IggmusPk	MEL USF2	narrowPeak	MEL USF2 IgG-mus TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	136	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL USF2 IgG-mus TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL USF2\
subGroups view=Peaks factor=USF2 cellType=MEL control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsMelUsf2IggmusPk\
type narrowPeak\

wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6SigRep1	Spleen 8w S 1	bigWig 1.000000 373038.000000	Spleen Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	136	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Spleen 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=SPLEEN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqSpleenCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 373038.000000\

wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep2	Lg Intestine P 2	narrowPeak	Large Intestine DNaseI HS Peaks Rep 2 from ENCODE/UW	3	137	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Large Intestine DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Lg Intestine P 2\
subGroups view=Peaks age=ADULT8WKS cellType=LGINT sex=M strain=C57BL6 treatment=zNONE rep=rep2\
track wgEncodeUwDnaseLgintC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeLicrHistoneLiverH3k27me3MAdult8wksC57bl6StdPk	Liver 8w H3K27m3	broadPeak	Liver 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	137	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 8w H3K27m3\
subGroups view=Peaks age=A1DLT8W factor=H3K27ME3 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k27me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverE14halfAlnRep1	Liver E14.5 Aln 1	bam	Liver E14.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	137	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Liver E14.5 Aln 1\
subGroups view=Alignments age=E14HALF cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverE14halfAlnRep1\
type bam\

wgEncodeSydhTfbsMelUsf2IggmusSig	MEL USF2 Ig_m	bigWig 1.000000 99544.000000	MEL USF2 IgG_mus TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	137	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL USF2 IgG_mus TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL USF2 Ig_m\
subGroups view=Signal factor=USF2 cellType=MEL control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsMelUsf2IggmusSig\
type bigWig 1.000000 99544.000000\

wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6AlnRep1	T-Naive 8w A 1	bam	T-Naive Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	137	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel T-Naive Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel T-Naive 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=T1NAIVE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep2	Lg Intestine S 2	bigWig 1.000000 53963.000000	Large Intestine DNaseI HS Signal Rep 2 from ENCODE/UW	2	138	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Large Intestine DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Lg Intestine S 2\
subGroups view=Signal age=ADULT8WKS cellType=LGINT sex=M strain=C57BL6 treatment=zNONE rep=rep2\
track wgEncodeUwDnaseLgintC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 53963.000000\

wgEncodeLicrHistoneLiverH3k27me3MAdult8wksC57bl6StdSig	Liver 8w H3K27m3	bigWig 0.130000 64.220001	Liver 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	138	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 8w H3K27m3\
subGroups view=Signal age=A1DLT8W factor=H3K27ME3 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k27me3MAdult8wksC57bl6StdSig\
type bigWig 0.130000 64.220001\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep1	Liver E14.5 - 1	bigWig 1.000000 14246225.000000	Liver E14.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	138	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Liver E14.5 - 1\
subGroups view=MinusRawSignal age=E14HALF cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep1\
type bigWig 1.000000 14246225.000000\

wgEncodeSydhTfbsMelUsf2IggrabPk	MEL USF2	narrowPeak	MEL USF2 IgG-rab TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	138	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL USF2 IgG-rab TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL USF2\
subGroups view=Peaks factor=USF2 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelUsf2IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6MinusRawRep1	T-Naive 8w MR 1	bigWig 1.000000 84237.000000	T-Naive Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	138	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel T-Naive Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel T-Naive 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=T1NAIVE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 84237.000000\

wgEncodeLicrHistoneLiverH3k36me3MAdult8wksC57bl6StdPk	Liver 8w H3K36m3	broadPeak	Liver 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	139	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 8w H3K36m3\
subGroups view=Peaks age=A1DLT8W factor=H3K36ME3 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k36me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep1	Liver E14.5 + 1	bigWig 1.000000 15356158.000000	Liver E14.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	139	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Liver E14.5 + 1\
subGroups view=PlusRawSignal age=E14HALF cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep1\
type bigWig 1.000000 15356158.000000\

wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep1	Livr C A8w H 1	broadPeak	Liver C57BL/6 Adult 8 Weeks DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	139	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver C57BL/6 Adult 8 Weeks DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Livr C A8w H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=LIVER sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeSydhTfbsMelUsf2IggrabSig	MEL USF2 Ig_r	bigWig 1.000000 117808.000000	MEL USF2 IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	139	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL USF2 IgG-rab TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL USF2 Ig_r\
subGroups view=Signal factor=USF2 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelUsf2IggrabSig\
type bigWig 1.000000 117808.000000\

wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6PlusRawRep1	T-Naive 8w PR 1	bigWig 1.000000 69036.000000	T-Naive Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	139	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel T-Naive Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel T-Naive 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=T1NAIVE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 69036.000000\

wgEncodeLicrHistoneLiverH3k36me3MAdult8wksC57bl6StdSig	Liver 8w H3K36m3	bigWig 0.120000 21.610001	Liver 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	140	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 8w H3K36m3\
subGroups view=Signal age=A1DLT8W factor=H3K36ME3 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k36me3MAdult8wksC57bl6StdSig\
type bigWig 0.120000 21.610001\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqLiverE14halfAlnRep2	Liver E14.5 Aln 2	bam	Liver E14.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	140	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Liver E14.5 Aln 2\
subGroups view=Alignments age=E14HALF cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverE14halfAlnRep2\
type bam\

wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep1	Livr C A8w P 1	narrowPeak	Liver C57BL/6 Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW	3	140	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver C57BL/6 Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Livr C A8w P 1\
subGroups view=Peaks age=ADULT8WKS cellType=LIVER sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeSydhTfbsMelZc3h11anb10074650IggrabPk	MEL ZC3H11A P	narrowPeak	MEL ZC3H11A (NB100-74650) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	140	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL ZC3H11A (NB100-74650) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL ZC3H11A P\
subGroups view=Peaks factor=ZC3H11ANB10074650 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelZc3h11anb10074650IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6SigRep1	T-Naive 8w S 1	bigWig 1.000000 84237.000000	T-Naive Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	140	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel T-Naive Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel T-Naive 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=T1NAIVE localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqTnaiveCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 84237.000000\

wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdPk	Liver 8w H3K79m2	broadPeak	Liver 8w H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	141	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 8w H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel Liver 8w H3K79m2\
subGroups view=Peaks age=A1DLT8W factor=H3K79ME2 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep2	Liver E14.5 - 2	bigWig 1.000000 12442109.000000	Liver E14.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	141	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Liver E14.5 - 2\
subGroups view=MinusRawSignal age=E14HALF cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverE14halfMinusRawRep2\
type bigWig 1.000000 12442109.000000\

wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep1	Livr C A8w S 1	bigWig 1.000000 49169.000000	Liver C57BL/6 Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW	2	141	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL/6 Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Livr C A8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=LIVER sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 49169.000000\

wgEncodeSydhTfbsMelZc3h11anb10074650IggrabSig	MEL ZC3H11A S	bigWig 1.000000 415.000000	MEL ZC3H11A (NB100-74650) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	141	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL ZC3H11A (NB100-74650) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL ZC3H11A S\
subGroups view=Signal factor=ZC3H11ANB10074650 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelZc3h11anb10074650IggrabSig\
type bigWig 1.000000 415.000000\

wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep1	Thymus 8w A 1	bam	Thymus Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW	0	141	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Thymus 8w A 1\
subGroups view=Alignments age=ADULT8WKS cellType=T2HYMUS localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep1\
type bam\

wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdSig	Liver 8w H3K79m2	bigWig 0.120000 51.799999	Liver 8w H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	142	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel Liver 8w H3K79m2\
subGroups view=Signal age=A1DLT8W factor=H3K79ME2 cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverH3k79me2MAdult8wksC57bl6StdSig\
type bigWig 0.120000 51.799999\
viewLimits 0.2:3\

wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep2	Liver E14.5 + 2	bigWig 1.000000 25603984.000000	Liver E14.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	142	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Liver E14.5 + 2\
subGroups view=PlusRawSignal age=E14HALF cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverE14halfPlusRawRep2\
type bigWig 1.000000 25603984.000000\

wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep2	Livr C A8w H 2	broadPeak	Liver C57BL/6 Adult 8 Weeks DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	142	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver C57BL/6 Adult 8 Weeks DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Livr C A8w H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=LIVER sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseLiverC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeSydhTfbsMelZkscan1hpa006672IggrabPk	MEL ZKSCAN1_H	narrowPeak	MEL ZKSCAN1 (HPA006672) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	142	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL ZKSCAN1 (HPA006672) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL ZKSCAN1_H\
subGroups view=Peaks factor=ZKSCAN1HPA006672 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelZkscan1hpa006672IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep2	Thymus 8w A 2	bam	Thymus Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW	0	142	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Thymus 8w A 2\
subGroups view=Alignments age=ADULT8WKS cellType=T2HYMUS localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6AlnRep2\
type bam\

wgEncodeLicrHistoneLiverInputMAdult8wksC57bl6StdSig	Liver 8w Input	bigWig 0.130000 65.070000	Liver 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	143	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Liver 8w Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=LIVER control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLiverInputMAdult8wksC57bl6StdSig\
type bigWig 0.130000 65.070000\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqLiverE14halfContigs	Liver E14.5 C	bed 6 +	Liver E14.5 Long RNA-seq Contigs from ENCODE/CSHL	3	143	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14.5 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Liver E14.5 C\
subGroups view=Contigs age=E14HALF cellType=LIVER rep=repP\
track wgEncodeCshlLongRnaSeqLiverE14halfContigs\
type bed 6 +\

wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep2	Livr C A8w P 2	narrowPeak	Liver C57BL/6 Adult 8 Weeks DNaseI HS Peaks Rep 2 from ENCODE/UW	3	143	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver C57BL/6 Adult 8 Weeks DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Livr C A8w P 2\
subGroups view=Peaks age=ADULT8WKS cellType=LIVER sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseLiverC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeSydhTfbsMelZkscan1hpa006672IggrabSig	MEL ZKSCAN1_H	bigWig 1.000000 71187.000000	MEL ZKSCAN1 (HPA006672) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	143	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL ZKSCAN1 (HPA006672) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL ZKSCAN1_H\
subGroups view=Signal factor=ZKSCAN1HPA006672 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelZkscan1hpa006672IggrabSig\
type bigWig 1.000000 71187.000000\

wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep1	Thymus 8w MR 1	bigWig 1.000000 25819.000000	Thymus Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	143	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Thymus 8w MR 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=T2HYMUS localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep1\
type bigWig 1.000000 25819.000000\

wgEncodeLicrHistoneLiverInputUE14halfC57bl6StdSig	Liver 14.5 Input	bigWig 0.130000 48.360001	Liver E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	144	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Liver 14.5 Input\
subGroups view=Signal age=E14HALF factor=INPUT cellType=LIVER control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneLiverInputUE14halfC57bl6StdSig\
type bigWig 0.130000 48.360001\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqLiverE14halfJunctions	Liver E14.5 J	bed 6 +	Liver E14.5 Long RNA-seq Junctions from ENCODE/CSHL	0	144	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E14.5 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Liver E14.5 J\
subGroups view=SJunctions age=E14HALF cellType=LIVER rep=repP\
track wgEncodeCshlLongRnaSeqLiverE14halfJunctions\
type bed 6 +\

wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2	Livr C A8w S 2	bigWig 1.000000 29008.000000	Liver C57BL/6 Adult 8 Weeks DNaseI HS Signal Rep 2 from ENCODE/UW	2	144	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL/6 Adult 8 Weeks DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Livr C A8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=LIVER sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 29008.000000\

wgEncodeSydhTfbsMelZnf384hpa004051IggrabPk	MEL ZNF384 P	narrowPeak	MEL ZNF384 (HPA004051) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	144	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL ZNF384 (HPA004051) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL ZNF384 P\
subGroups view=Peaks factor=ZNF384HPA004051 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelZnf384hpa004051IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep2	Thymus 8w MR 2	bigWig 1.000000 42756.000000	Thymus Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	144	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Thymus 8w MR 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=T2HYMUS localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6MinusRawRep2\
type bigWig 1.000000 42756.000000\

wgEncodeCshlLongRnaSeqLiverE18AlnRep1	Liver E18 Aln 1	bam	Liver E18 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	145	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E18 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Liver E18 Aln 1\
subGroups view=Alignments age=E18 cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverE18AlnRep1\
type bam\

wgEncodeUwDnaseLiverC57bl6ME14halfHotspotsRep1	Livr C E14.5 H 1	broadPeak	Liver C57BL/6 Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	145	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver C57BL/6 Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Livr C E14.5 H 1\
subGroups view=Hotspots age=E14HALF cellType=LIVER sex=M strain=C57BL6 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseLiverC57bl6ME14halfHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdPk	Lung H3K4m1	broadPeak	Lung 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	145	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Lung H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsMelZnf384hpa004051IggrabSig	MEL ZNF384 S	bigWig 1.000000 37249.000000	MEL ZNF384 (HPA004051) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	145	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL ZNF384 (HPA004051) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL ZNF384 S\
subGroups view=Signal factor=ZNF384HPA004051 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelZnf384hpa004051IggrabSig\
type bigWig 1.000000 37249.000000\

wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep1	Thymus 8w PR 1	bigWig 1.000000 16221.000000	Thymus Adult 8 weeks RNA-seq Plus Raw signal Rep 1 from ENCODE/UW	2	145	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Plus Raw signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Thymus 8w PR 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=T2HYMUS localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep1\
type bigWig 1.000000 16221.000000\

wgEncodeCshlLongRnaSeqLiverE18MinusRawRep1	Liver E18 - 1	bigWig 1.000000 8260340.000000	Liver E18 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	146	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E18 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Liver E18 - 1\
subGroups view=MinusRawSignal age=E18 cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverE18MinusRawRep1\
type bigWig 1.000000 8260340.000000\

wgEncodeUwDnaseLiverC57bl6ME14halfPkRep1	Livr C E14.5 P 1	narrowPeak	Liver C57BL/6 Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	146	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver C57BL/6 Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Livr C E14.5 P 1\
subGroups view=Peaks age=E14HALF cellType=LIVER sex=M strain=C57BL6 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseLiverC57bl6ME14halfPkRep1\
type narrowPeak\

wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdSig	Lung H3K4m1	bigWig 0.130000 25.240000	Lung 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	146	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Lung H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLungH3k4me1MAdult8wksC57bl6StdSig\
type bigWig 0.130000 25.240000\
viewLimits 0.2:3\

wgEncodeSydhTfbsMelZnfmizdcp1ab65767IggrabPk	MEL ZNF-MIZD P	narrowPeak	MEL ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	146	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL ZNF-MIZD P\
subGroups view=Peaks factor=ZNFMIZDCP1AB65767 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelZnfmizdcp1ab65767IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep2	Thymus 8w PR 2	bigWig 1.000000 42518.000000	Thymus Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	146	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Thymus 8w PR 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=T2HYMUS localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6PlusRawRep2\
type bigWig 1.000000 42518.000000\

wgEncodeCshlLongRnaSeqLiverE18PlusRawRep1	Liver E18 + 1	bigWig 1.000000 8811002.000000	Liver E18 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	147	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E18 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Liver E18 + 1\
subGroups view=PlusRawSignal age=E18 cellType=LIVER rep=rep1\
track wgEncodeCshlLongRnaSeqLiverE18PlusRawRep1\
type bigWig 1.000000 8811002.000000\

wgEncodeUwDnaseLiverC57bl6ME14halfSigRep1	Livr C E14.5 S 1	bigWig 1.000000 148306.000000	Liver C57BL/6 Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW	2	147	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver C57BL/6 Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Livr C E14.5 S 1\
subGroups view=Signal age=E14HALF cellType=LIVER sex=M strain=C57BL6 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseLiverC57bl6ME14halfSigRep1\
type bigWig 1.000000 148306.000000\

wgEncodeLicrHistoneLungH3k4me3MAdult8wksC57bl6StdPk	Lung H3K4m3	broadPeak	Lung 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	147	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Lung H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLungH3k4me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsMelZnfmizdcp1ab65767IggrabSig	MEL ZNF-MIZD S	bigWig 1.000000 49986.000000	MEL ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	147	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL ZNF-MIZD-CP1 (ab65767) TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL ZNF-MIZD S\
subGroups view=Signal factor=ZNFMIZDCP1AB65767 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelZnfmizdcp1ab65767IggrabSig\
type bigWig 1.000000 49986.000000\

wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep1	Thymus 8w S 1	bigWig 1.000000 25819.000000	Thymus Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW	2	147	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Thymus 8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=T2HYMUS localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep1\
type bigWig 1.000000 25819.000000\

wgEncodeCshlLongRnaSeqLiverE18AlnRep2	Liver E18 Aln 2	bam	Liver E18 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	148	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E18 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Liver E18 Aln 2\
subGroups view=Alignments age=E18 cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverE18AlnRep2\
type bam\

wgEncodeUwDnaseLiverS129ME14halfHotspotsRep1	Livr 1 E14.5 H 1	broadPeak	Liver 129 Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	148	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 129 Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Livr 1 E14.5 H 1\
subGroups view=Hotspots age=E14HALF cellType=LIVER sex=M strain=a129 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseLiverS129ME14halfHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneLungH3k4me3MAdult8wksC57bl6StdSig	Lung H3K4m3	bigWig 0.120000 55.680000	Lung 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	148	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Lung H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLungH3k4me3MAdult8wksC57bl6StdSig\
type bigWig 0.120000 55.680000\
viewLimits 0.2:10\

wgEncodeSydhTfbsMelInputIggmusSig	MEL IgG-mus	bigWig 1 78618	MEL IgG-mus Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	148	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL IgG-mus Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL IgG-mus\
subGroups view=Signal factor=ZZZInputIGGMUS cellType=MEL control=IGGMUS treatment=zNONE\
track wgEncodeSydhTfbsMelInputIggmusSig\
type bigWig 1 78618\

wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep2	Thymus 8w S 2	bigWig 1.000000 42756.000000	Thymus Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW	2	148	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Thymus 8w S 2\
subGroups view=Signal age=ADULT8WKS cellType=T2HYMUS localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqThymusCellPolyaMAdult8wksC57bl6SigRep2\
type bigWig 1.000000 42756.000000\

wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep1	Brain E14.5 A 1	bam	Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/UW	0	149	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Brain E14.5 A 1\
subGroups view=Alignments age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep1\
type bam\

wgEncodeCshlLongRnaSeqLiverE18MinusRawRep2	Liver E18 - 2	bigWig 1.000000 6178518.000000	Liver E18 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	149	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E18 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Liver E18 - 2\
subGroups view=MinusRawSignal age=E18 cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverE18MinusRawRep2\
type bigWig 1.000000 6178518.000000\

wgEncodeUwDnaseLiverS129ME14halfPkRep1	Livr 1 E14.5 P 1	narrowPeak	Liver 129 Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	149	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 129 Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Livr 1 E14.5 P 1\
subGroups view=Peaks age=E14HALF cellType=LIVER sex=M strain=a129 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseLiverS129ME14halfPkRep1\
type narrowPeak\

wgEncodeLicrHistoneLungInputMAdult8wksC57bl6StdSig	Lung Input	bigWig 0.150000 39.330002	Lung 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	149	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Lung Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=LUNG control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneLungInputMAdult8wksC57bl6StdSig\
type bigWig 0.150000 39.330002\
viewLimits 0.2:5\

wgEncodeSydhTfbsMelInputIggrabSig	MEL IgG-rab	bigWig 1 103648	MEL IgG-rab Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	149	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL IgG-rab Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL IgG-rab\
subGroups view=Signal factor=ZZZInputIGGRAB cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelInputIggrabSig\
type bigWig 1 103648\

wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep1	Brain E18.5 A 1	bam	Whole Brain Embryonic day 18.5 RNA-seq Alignments Rep 1 from ENCODE/UW	0	150	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain Embryonic day 18.5 RNA-seq Alignments Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Brain E18.5 A 1\
subGroups view=Alignments age=E18HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep1\
type bam\

wgEncodeCshlLongRnaSeqLiverE18PlusRawRep2	Liver E18 + 2	bigWig 1.000000 7504586.000000	Liver E18 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	150	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver E18 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Liver E18 + 2\
subGroups view=PlusRawSignal age=E18 cellType=LIVER rep=rep2\
track wgEncodeCshlLongRnaSeqLiverE18PlusRawRep2\
type bigWig 1.000000 7504586.000000\

wgEncodeUwDnaseLiverS129ME14halfSigRep1	Livr 1 E14.5 S 1	bigWig 1.000000 98657.000000	Liver 129 Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW	2	150	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 129 Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Livr 1 E14.5 S 1\
subGroups view=Signal age=E14HALF cellType=LIVER sex=M strain=a129 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseLiverS129ME14halfSigRep1\
type bigWig 1.000000 98657.000000\

wgEncodeLicrHistoneMefH3k4me1MAdult8wksC57bl6StdPk	MEF H3K4m1	broadPeak	MEF 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	150	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel MEF 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel MEF H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMefH3k4me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsMelInputDm2p5dIggratSig	MEL Input D	bigWig 1.000000 87331.000000	MEL DMSO 2% Input IgG-rat TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	150	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL DMSO 2% Input IgG-rat TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Input D\
subGroups view=Signal factor=ZZZInputIGGRAT cellType=MEL control=IGGRAT treatment=DM2P5D\
track wgEncodeSydhTfbsMelInputDm2p5dIggratSig\
type bigWig 1.000000 87331.000000\

wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep2	Brain E14.5 A 2	bam	Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/UW	0	151	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Brain E14.5 A 2\
subGroups view=Alignments age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6AlnRep2\
type bam\

wgEncodeCshlLongRnaSeqLiverE18Contigs	Liver E18 C	bed 6 +	Liver E18 Long RNA-seq Contigs from ENCODE/CSHL	3	151	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E18 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Liver E18 C\
subGroups view=Contigs age=E18 cellType=LIVER rep=repP\
track wgEncodeCshlLongRnaSeqLiverE18Contigs\
type bed 6 +\

wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep1	Livr 1D E14.5 H 1	broadPeak	Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	151	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Livr 1D E14.5 H 1\
subGroups view=Hotspots age=E14HALF cellType=LIVER sex=M strain=a129DLCR treatment=zNONE rep=rep1\
track wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneMefH3k4me1MAdult8wksC57bl6StdSig	MEF H3K4m1	bigWig 0.110000 21.290001	MEF 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	151	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel MEF H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMefH3k4me1MAdult8wksC57bl6StdSig\
type bigWig 0.110000 21.290001\
viewLimits 0.2:3\

wgEncodeSydhTfbsMelInputIggratSig	MEL IgG-rat	bigWig 1 90844	MEL IgG-rat Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	151	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL IgG-rat Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL IgG-rat\
subGroups view=Signal factor=ZZZInputIGGRAT cellType=MEL control=IGGRAT treatment=zNONE\
track wgEncodeSydhTfbsMelInputIggratSig\
type bigWig 1 90844\

wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep2	Brain E18.5 A 2	bam	Whole Brain Embryonic day 18.5 RNA-seq Alignments Rep 2 from ENCODE/UW	0	152	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain Embryonic day 18.5 RNA-seq Alignments Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewAlignments off\
shortLabel Brain E18.5 A 2\
subGroups view=Alignments age=E18HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6AlnRep2\
type bam\

wgEncodeCshlLongRnaSeqLiverE18Junctions	Liver E18 J	bed 6 +	Liver E18 Long RNA-seq Junctions from ENCODE/CSHL	0	152	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver E18 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Liver E18 J\
subGroups view=SJunctions age=E18 cellType=LIVER rep=repP\
track wgEncodeCshlLongRnaSeqLiverE18Junctions\
type bed 6 +\

wgEncodeUwDnaseLiver129dlcrME14halfPkRep1	Livr 1D E14.5 P 1	narrowPeak	Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	152	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Livr 1D E14.5 P 1\
subGroups view=Peaks age=E14HALF cellType=LIVER sex=M strain=a129DLCR treatment=zNONE rep=rep1\
track wgEncodeUwDnaseLiver129dlcrME14halfPkRep1\
type narrowPeak\

wgEncodeLicrHistoneMefH3k4me3MAdult8wksC57bl6StdPk	MEF H3K4m3	broadPeak	MEF 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	152	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel MEF 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel MEF H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMefH3k4me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsMelInputDm2p5dIggyaleSig	MEL IgG-Y D	bigWig 1.000000 78459.000000	MEL IgG-Yale Input DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	152	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL IgG-Yale Input DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL IgG-Y D\
subGroups view=Signal factor=ZZZInputIGGYALE cellType=MEL control=IGGYALE treatment=DM2P5D\
track wgEncodeSydhTfbsMelInputDm2p5dIggyaleSig\
type bigWig 1.000000 78459.000000\

wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep1	Brain E14.5 MR 1	bigWig 1.000000 24820.000000	Whole Brain Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	153	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Brain E14.5 MR 1\
subGroups view=MinusRawSignal age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep1\
type bigWig 1.000000 24820.000000\

wgEncodeUwDnaseLiver129dlcrME14halfSigRep1	Livr 1D E14.5 S 1	bigWig 1.000000 113387.000000	Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW	2	153	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Livr 1D E14.5 S 1\
subGroups view=Signal age=E14HALF cellType=LIVER sex=M strain=a129DLCR treatment=zNONE rep=rep1\
track wgEncodeUwDnaseLiver129dlcrME14halfSigRep1\
type bigWig 1.000000 113387.000000\

wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep1V2	Lung Aln 1	bam	Lung A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	153	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Lung Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=LUNG rep=rep1\
track wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep1V2\
type bam\

wgEncodeLicrHistoneMefH3k4me3MAdult8wksC57bl6StdSig	MEF H3K4m3	bigWig 0.130000 71.599998	MEF 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	153	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel MEF H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMefH3k4me3MAdult8wksC57bl6StdSig\
type bigWig 0.130000 71.599998\
viewLimits 0.2:10\

wgEncodeSydhTfbsMelInputDm2p5dStdSigV2	MEL Input D	bigWig 1.000000 84376.000000	MEL Input DMSO 2% ChIP-seq Signal from ENCODE/Stanford/Yale	2	153	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Input DMSO 2% ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Input D\
subGroups view=Signal factor=ZZZInputstd cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhTfbsMelInputDm2p5dStdSigV2\
type bigWig 1.000000 84376.000000\

wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep1	Brain E18.5 MR 1	bigWig 1.000000 89685.000000	Whole Brain Embryonic day 18.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW	2	154	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 18.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Brain E18.5 MR 1\
subGroups view=MinusRawSignal age=E18HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep1\
type bigWig 1.000000 89685.000000\

wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep2	Livr 1D E14.5 H 2	broadPeak	Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	154	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Livr 1D E14.5 H 2\
subGroups view=Hotspots age=E14HALF cellType=LIVER sex=M strain=a129DLCR treatment=zNONE rep=rep2\
track wgEncodeUwDnaseLiver129dlcrME14halfHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep1	Lung - 1	bigWig 1.000000 1083071.000000	Lung A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	154	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Lung - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LUNG rep=rep1\
track wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep1\
type bigWig 1.000000 1083071.000000\

wgEncodeLicrHistoneMefH3k27acMAdult8wksC57bl6StdPk	MEF H3K27a	broadPeak	MEF 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	154	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel MEF 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel MEF H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMefH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeSydhTfbsMelInputDm2p5dStdSig	MEL Input D	bigWig 1.000000 103298.000000	MEL Standard Input DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	154	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Standard Input DMSO 2% TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Input D\
subGroups view=Signal factor=ZZZInputstd cellType=MEL control=STD treatment=DM2P5D\
track wgEncodeSydhTfbsMelInputDm2p5dStdSig\
type bigWig 1.000000 103298.000000\

wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep2	Brain E14.5 MR 2	bigWig 1.000000 19618.000000	Whole Brain Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	155	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Brain E14.5 MR 2\
subGroups view=MinusRawSignal age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6MinusRawRep2\
type bigWig 1.000000 19618.000000\

wgEncodeUwDnaseLiver129dlcrME14halfPkRep2	Livr 1D E14.5 P 2	narrowPeak	Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Peaks Rep 2 from ENCODE/UW	3	155	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Livr 1D E14.5 P 2\
subGroups view=Peaks age=E14HALF cellType=LIVER sex=M strain=a129DLCR treatment=zNONE rep=rep2\
track wgEncodeUwDnaseLiver129dlcrME14halfPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep1	Lung + 1	bigWig 1.000000 662082.000000	Lung A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	155	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Lung + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LUNG rep=rep1\
track wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep1\
type bigWig 1.000000 662082.000000\

wgEncodeLicrHistoneMefH3k27acMAdult8wksC57bl6StdSig	MEF H3K27a	bigWig 0.130000 43.160000	MEF 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	155	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel MEF H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMefH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.130000 43.160000\
viewLimits 0.2:5\

wgEncodeSydhTfbsMelInputStdSig	MEL Input	bigWig 1.000000 132487.000000	MEL Standard Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	155	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Standard Input TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL Input\
subGroups view=Signal factor=ZZZInputstd cellType=MEL control=STD treatment=zNONE\
track wgEncodeSydhTfbsMelInputStdSig\
type bigWig 1.000000 132487.000000\

wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep2	Brain E18.5 MR 2	bigWig 1.000000 30690.000000	Whole Brain Embryonic day 18.5 RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW	2	156	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 18.5 RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewMinusRawSig off\
shortLabel Brain E18.5 MR 2\
subGroups view=MinusRawSignal age=E18HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6MinusRawRep2\
type bigWig 1.000000 30690.000000\

wgEncodeUwDnaseLiver129dlcrME14halfSigRep2	Livr 1D E14.5 S 2	bigWig 1.000000 126964.000000	Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Signal Rep 2 from ENCODE/UW	2	156	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Liver 129.DLCR/DLCR Embryonic Day 14.5 DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Livr 1D E14.5 S 2\
subGroups view=Signal age=E14HALF cellType=LIVER sex=M strain=a129DLCR treatment=zNONE rep=rep2\
track wgEncodeUwDnaseLiver129dlcrME14halfSigRep2\
type bigWig 1.000000 126964.000000\

wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep2V2	Lung Aln 2	bam	Lung A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	156	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Lung Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=LUNG rep=rep2\
track wgEncodeCshlLongRnaSeqLungAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistoneMefInputMAdult8wksC57bl6StdSig	MEF Input	bigWig 0.140000 50.770000	MEF 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	156	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel MEF 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel MEF Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=MEF control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMefInputMAdult8wksC57bl6StdSig\
type bigWig 0.140000 50.770000\
viewLimits 0.2:5\

wgEncodeSydhTfbsMelCmybsc7874IggrabPk	MEL c-Myb	narrowPeak	MEL c-Myb TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	156	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL c-Myb TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL c-Myb\
subGroups view=Peaks factor=cMYBSC7874 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelCmybsc7874IggrabPk\
type narrowPeak\

wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep1	Brain E14.5 PR 1	bigWig 1.000000 29009.000000	Whole Brain Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	157	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Brain E14.5 PR 1\
subGroups view=PlusRawSignal age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep1\
type bigWig 1.000000 29009.000000\

wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep2	Lung - 2	bigWig 1.000000 1199651.000000	Lung A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	157	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Lung - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=LUNG rep=rep2\
track wgEncodeCshlLongRnaSeqLungAdult8wksMinusRawRep2\
type bigWig 1.000000 1199651.000000\

wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep1	Lung H 1	broadPeak	Lung DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	157	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Lung H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=LUNG sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeSydhTfbsMelCmybsc7874IggrabSig	MEL c-Myb	bigWig 1.000000 106720.000000	MEL c-Myb TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	157	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL c-Myb TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL c-Myb\
subGroups view=Signal factor=cMYBSC7874 cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelCmybsc7874IggrabSig\
type bigWig 1.000000 106720.000000\

wgEncodeLicrHistoneMelH3k04me1MImmortalC57bl6StdPk	MEL H3K4m1	broadPeak	MEL H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	157	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel MEL H3K4m1\
subGroups view=Peaks age=IMMORTAL factor=H3K04ME1 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k04me1MImmortalC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep1	Brain E18.5 PR 1	bigWig 1.000000 177309.000000	Whole Brain Embryonic day 18.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW	2	158	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 18.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Brain E18.5 PR 1\
subGroups view=PlusRawSignal age=E18HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep1\
type bigWig 1.000000 177309.000000\

wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep2	Lung + 2	bigWig 1.000000 852123.000000	Lung A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	158	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Lung + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=LUNG rep=rep2\
track wgEncodeCshlLongRnaSeqLungAdult8wksPlusRawRep2\
type bigWig 1.000000 852123.000000\

wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep1	Lung P 1	narrowPeak	Lung DNaseI HS Peaks Rep 1 from ENCODE/UW	3	158	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Lung P 1\
subGroups view=Peaks age=ADULT8WKS cellType=LUNG sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeSydhTfbsMelCmycIggrabPk	MEL c-Myc	narrowPeak	MEL c-Myc TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale	3	158	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL c-Myc TFBS ChIP-seq Peaks from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewPeaks off\
shortLabel MEL c-Myc\
subGroups view=Peaks factor=cMYC cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelCmycIggrabPk\
type narrowPeak\

wgEncodeLicrHistoneMelH3k04me1MImmortalC57bl6StdSig	MEL H3K4m1	bigWig 0.150000 33.680000	MEL H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	158	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel MEL H3K4m1\
subGroups view=Signal age=IMMORTAL factor=H3K04ME1 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k04me1MImmortalC57bl6StdSig\
type bigWig 0.150000 33.680000\
viewLimits 0.2:3\

wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep2	Brain E14.5 PR 2	bigWig 1.000000 46115.000000	Whole Brain Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	159	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Brain E14.5 PR 2\
subGroups view=PlusRawSignal age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6PlusRawRep2\
type bigWig 1.000000 46115.000000\

wgEncodeCshlLongRnaSeqLungAdult8wksContigs	Lung C	bed 6 +	Lung A8 Long RNA-seq Contigs from ENCODE/CSHL	3	159	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Lung C\
subGroups view=Contigs age=ADULT8WKS cellType=LUNG rep=repP\
track wgEncodeCshlLongRnaSeqLungAdult8wksContigs\
type bed 6 +\

wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep1	Lung S 1	bigWig 1.000000 33112.000000	Lung DNaseI HS Signal Rep 1 from ENCODE/UW	2	159	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Lung S 1\
subGroups view=Signal age=ADULT8WKS cellType=LUNG sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 33112.000000\

wgEncodeSydhTfbsMelCmycIggrabSig	MEL c-Myc	bigWig 1 61932	MEL c-Myc TFBS ChIP-seq Signal from ENCODE/Stanford/Yale	2	159	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL c-Myc TFBS ChIP-seq Signal from ENCODE/Stanford/Yale\
parent wgEncodeSydhTfbsViewSig off\
shortLabel MEL c-Myc\
subGroups view=Signal factor=cMYC cellType=MEL control=IGGRAB treatment=zNONE\
track wgEncodeSydhTfbsMelCmycIggrabSig\
type bigWig 1 61932\

wgEncodeLicrHistoneMelH3k04me3MImmortalC57bl6StdPk	MEL H3K4m3	broadPeak	MEL H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	159	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel MEL H3K4m3\
subGroups view=Peaks age=IMMORTAL factor=H3K04ME3 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k04me3MImmortalC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep2	Brain E18.5 PR 2	bigWig 1.000000 36131.000000	Whole Brain Embryonic day 18.5 RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW	2	160	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 18.5 RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewPlusRawSig off\
shortLabel Brain E18.5 PR 2\
subGroups view=PlusRawSignal age=E18HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6PlusRawRep2\
type bigWig 1.000000 36131.000000\

wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep2	Lung H 2	broadPeak	Lung DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	160	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Lung H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=LUNG sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseLungC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqLungAdult8wksJunctions	Lung J	bed 6 +	Lung A8 Long RNA-seq Junctions from ENCODE/CSHL	0	160	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Lung J\
subGroups view=SJunctions age=ADULT8WKS cellType=LUNG rep=repP\
track wgEncodeCshlLongRnaSeqLungAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneMelH3k04me3MImmortalC57bl6StdSig	MEL H3K4m3	bigWig 0.110000 82.040001	MEL H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	160	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel MEL H3K4m3\
subGroups view=Signal age=IMMORTAL factor=H3K04ME3 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k04me3MImmortalC57bl6StdSig\
type bigWig 0.110000 82.040001\
viewLimits 0.2:10\

wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep1	Brain E14.5 S 1	bigWig 1.000000 29009.000000	Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/UW	2	161	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Brain E14.5 S 1\
subGroups view=Signal age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep1\
type bigWig 1.000000 29009.000000\

wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep2	Lung P 2	narrowPeak	Lung DNaseI HS Peaks Rep 2 from ENCODE/UW	3	161	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Lung DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Lung P 2\
subGroups view=Peaks age=ADULT8WKS cellType=LUNG sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseLungC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep1V2	MaGland Aln 1	bam	Mammary Gland A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	161	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Mammary Gland A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel MaGland Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=MAMG rep=rep1\
track wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep1V2\
type bam\

wgEncodeLicrHistoneMelH3k09acMImmortalC57bl6StdPk	MEL H3K9a	broadPeak	MEL H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	161	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K9ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel MEL H3K9a\
subGroups view=Peaks age=IMMORTAL factor=H3K09AC cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k09acMImmortalC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep1	Brain E18.5 S 1	bigWig 1.000000 177309.000000	Whole Brain Embryonic day 18.5 RNA-seq Signal Rep 1 from ENCODE/UW	2	162	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 18.5 RNA-seq Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Brain E18.5 S 1\
subGroups view=Signal age=E18HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep1\
track wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep1\
type bigWig 1.000000 177309.000000\

wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep2	Lung S 2	bigWig 1.000000 34840.000000	Lung DNaseI HS Signal Rep 2 from ENCODE/UW	2	162	0	0	0	127	127	127	0	0	0				regulation	0	longLabel Lung DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Lung S 2\
subGroups view=Signal age=ADULT8WKS cellType=LUNG sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseLungC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 34840.000000\

wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep1	MaGland - 1	bigWig 1.000000 844027.000000	Mammary Gland A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	162	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Mammary Gland A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel MaGland - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=MAMG rep=rep1\
track wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep1\
type bigWig 1.000000 844027.000000\

wgEncodeLicrHistoneMelH3k09acMImmortalC57bl6StdSig	MEL H3K9a	bigWig 0.130000 69.959999	MEL H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	162	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K9ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel MEL H3K9a\
subGroups view=Signal age=IMMORTAL factor=H3K09AC cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k09acMImmortalC57bl6StdSig\
type bigWig 0.130000 69.959999\
viewLimits 0.2:5\

wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep2	Brain E14.5 S 2	bigWig 1.000000 46115.000000	Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/UW	2	163	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Brain E14.5 S 2\
subGroups view=Signal age=E14HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqWbrainCellPolyaME14halfC57bl6SigRep2\
type bigWig 1.000000 46115.000000\

wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep1	MaGland + 1	bigWig 1.000000 1249790.000000	Mammary Gland A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	163	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Mammary Gland A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel MaGland + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=MAMG rep=rep1\
track wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep1\
type bigWig 1.000000 1249790.000000\

wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep1	MEL H 1	broadPeak	MEL DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	163	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots\
shortLabel MEL H 1\
subGroups view=Hotspots age=IMMORTAL cellType=MEL sex=M strain=UKN rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneMelH3k27acMImmortalC57bl6StdPk	MEL H3K27a	broadPeak	MEL H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	163	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel MEL H3K27a\
subGroups view=Peaks age=IMMORTAL factor=H3K27AC cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k27acMImmortalC57bl6StdPk\
type broadPeak\

wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep2	Brain E18.5 S 2	bigWig 1.000000 36131.000000	Whole Brain Embryonic day 18.5 RNA-seq Signal Rep 2 from ENCODE/UW	2	164	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Embryonic day 18.5 RNA-seq Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwRnaSeqViewSignal off\
shortLabel Brain E18.5 S 2\
subGroups view=Signal age=E18HALF cellType=WBRAIN localization=CELL rnaExtract=POLYA sex=M strain=C57BL6 rep=rep2\
track wgEncodeUwRnaSeqWbrainCellPolyaME18halfC57bl6SigRep2\
type bigWig 1.000000 36131.000000\

wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep2V2	MaGland Aln 2	bam	Mammary Gland A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	164	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Mammary Gland A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel MaGland Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=MAMG rep=rep2\
track wgEncodeCshlLongRnaSeqMamgAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistoneMelH3k27acMImmortalC57bl6StdSig	MEL H3K27a	bigWig 0.150000 73.129997	MEL H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	164	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel MEL H3K27a\
subGroups view=Signal age=IMMORTAL factor=H3K27AC cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k27acMImmortalC57bl6StdSig\
type bigWig 0.150000 73.129997\
viewLimits 0.2:5\

wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep1	MEL P 1	narrowPeak	MEL DNaseI HS Peaks Rep 1 from ENCODE/UW	3	164	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks\
shortLabel MEL P 1\
subGroups view=Peaks age=IMMORTAL cellType=MEL sex=M strain=UKN rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep2	MaGland - 2	bigWig 1.000000 267141.000000	Mammary Gland A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	165	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Mammary Gland A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel MaGland - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=MAMG rep=rep2\
track wgEncodeCshlLongRnaSeqMamgAdult8wksMinusRawRep2\
type bigWig 1.000000 267141.000000\

wgEncodeLicrHistoneMelH3k27me3MImmortalC57bl6StdPk	MEL H3K27m3	broadPeak	MEL H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	165	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel MEL H3K27m3\
subGroups view=Peaks age=IMMORTAL factor=H3K27ME3 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k27me3MImmortalC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep1	MEL S 1	bigWig 1.000000 123367.000000	MEL DNaseI HS Signal Rep 1 from ENCODE/UW	2	165	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal\
shortLabel MEL S 1\
subGroups view=Signal age=IMMORTAL cellType=MEL sex=M strain=UKN rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 123367.000000\

wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep2	MaGland + 2	bigWig 1.000000 712426.000000	Mammary Gland A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	166	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Mammary Gland A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel MaGland + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=MAMG rep=rep2\
track wgEncodeCshlLongRnaSeqMamgAdult8wksPlusRawRep2\
type bigWig 1.000000 712426.000000\

wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep2	MEL H 2	broadPeak	MEL DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	166	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel MEL H 2\
subGroups view=Hotspots age=IMMORTAL cellType=MEL sex=M strain=UKN rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseMelC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneMelH3k27me3MImmortalC57bl6StdSig	MEL H3K27m3	bigWig 0.110000 35.549999	MEL H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	166	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel MEL H3K27m3\
subGroups view=Signal age=IMMORTAL factor=H3K27ME3 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k27me3MImmortalC57bl6StdSig\
type bigWig 0.110000 35.549999\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqMamgAdult8wksContigs	MaGland C	bed 6 +	Mammary Gland A8 Long RNA-seq Contigs from ENCODE/CSHL	3	167	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Mammary Gland A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel MaGland C\
subGroups view=Contigs age=ADULT8WKS cellType=MAMG rep=repP\
track wgEncodeCshlLongRnaSeqMamgAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneMelH3k36me3MImmortalC57bl6StdPk	MEL H3K36m3	broadPeak	MEL H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	167	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel MEL H3K36m3\
subGroups view=Peaks age=IMMORTAL factor=H3K36ME3 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k36me3MImmortalC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep2	MEL P 2	narrowPeak	MEL DNaseI HS Peaks Rep 2 from ENCODE/UW	3	167	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel MEL P 2\
subGroups view=Peaks age=IMMORTAL cellType=MEL sex=M strain=UKN rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseMelC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqMamgAdult8wksJunctions	MaGland J	bed 6 +	Mammary Gland A8 Long RNA-seq Junctions from ENCODE/CSHL	0	168	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Mammary Gland A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel MaGland J\
subGroups view=SJunctions age=ADULT8WKS cellType=MAMG rep=repP\
track wgEncodeCshlLongRnaSeqMamgAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneMelH3k36me3MImmortalC57bl6StdSig	MEL H3K36m3	bigWig 0.110000 21.510000	MEL H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	168	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel MEL H3K36m3\
subGroups view=Signal age=IMMORTAL factor=H3K36ME3 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k36me3MImmortalC57bl6StdSig\
type bigWig 0.110000 21.510000\
viewLimits 0.2:2\

wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep2	MEL S 2	bigWig 1.000000 228690.000000	MEL DNaseI HS Signal Rep 2 from ENCODE/UW	2	168	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel MEL S 2\
subGroups view=Signal age=IMMORTAL cellType=MEL sex=M strain=UKN rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseMelC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 228690.000000\

wgEncodeLicrHistoneMelH3k79me2MImmortalC57bl6StdPk	MEL H3K79m2	broadPeak	MEL H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	169	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel MEL H3K79me2 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks\
shortLabel MEL H3K79m2\
subGroups view=Peaks age=IMMORTAL factor=H3K79ME2 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k79me2MImmortalC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep1	Mesoderm H 1	broadPeak	Mesoderm DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	169	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel Mesoderm DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Mesoderm H 1\
subGroups view=Hotspots age=E11HALF cellType=MESODERM sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep1V2	Ovary Aln 1	bam	Ovary A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	169	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Ovary A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Ovary Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=OVARY rep=rep1\
track wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep1V2\
type bam\

wgEncodeLicrHistoneMelH3k79me2MImmortalC57bl6StdSig	MEL H3K79m2	bigWig 0.110000 44.459999	MEL H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	170	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL H3K79me2 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal\
shortLabel MEL H3K79m2\
subGroups view=Signal age=IMMORTAL factor=H3K79ME2 cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelH3k79me2MImmortalC57bl6StdSig\
type bigWig 0.110000 44.459999\
viewLimits 0.2:3\

wgEncodeUwDnaseMesodermCd1ME11halfPkRep1	Mesoderm P 1	narrowPeak	Mesoderm DNaseI HS Peaks Rep 1 from ENCODE/UW	3	170	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel Mesoderm DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Mesoderm P 1\
subGroups view=Peaks age=E11HALF cellType=MESODERM sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseMesodermCd1ME11halfPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep1	Ovary - 1	bigWig 1.000000 111584.000000	Ovary A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	170	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Ovary A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel Ovary - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=OVARY rep=rep1\
track wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep1\
type bigWig 1.000000 111584.000000\

wgEncodeLicrHistoneMelInputMImmortalC57bl6StdSig	MEL Input	bigWig 0.150000 92.559998	MEL Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	171	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel MEL Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel MEL Input\
subGroups view=Signal age=IMMORTAL factor=INPUT cellType=MEL control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneMelInputMImmortalC57bl6StdSig\
type bigWig 0.150000 92.559998\
viewLimits 0.2:5\

wgEncodeUwDnaseMesodermCd1ME11halfSigRep1	Mesoderm S 1	bigWig 1.000000 267460.000000	Mesoderm DNaseI HS Signal Rep 1 from ENCODE/UW	2	171	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel Mesoderm DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Mesoderm S 1\
subGroups view=Signal age=E11HALF cellType=MESODERM sex=M strain=CD1 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseMesodermCd1ME11halfSigRep1\
type bigWig 1.000000 267460.000000\

wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep1	Ovary + 1	bigWig 1.000000 243375.000000	Ovary A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	171	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Ovary A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Ovary + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=OVARY rep=rep1\
track wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep1\
type bigWig 1.000000 243375.000000\

wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep2	Mesoderm H 2	broadPeak	Mesoderm DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	172	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel Mesoderm DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Mesoderm H 2\
subGroups view=Hotspots age=E11HALF cellType=MESODERM sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseMesodermCd1ME11halfHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneOlfactH3k04me1MAdult8wksC57bl6StdPk	Olfact H3K4m1	broadPeak	Olfactory Bulb 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	172	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Olfactory Bulb 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Olfact H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneOlfactH3k04me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep2V2	Ovary Aln 2	bam	Ovary A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	172	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Ovary A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Ovary Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=OVARY rep=rep2\
track wgEncodeCshlLongRnaSeqOvaryAdult8wksAlnRep2V2\
type bam\

wgEncodeUwDnaseMesodermCd1ME11halfPkRep2	Mesoderm P 2	narrowPeak	Mesoderm DNaseI HS Peaks Rep 2 from ENCODE/UW	3	173	65	105	225	160	180	240	0	0	0				regulation	1	color 65,105,225\
longLabel Mesoderm DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Mesoderm P 2\
subGroups view=Peaks age=E11HALF cellType=MESODERM sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseMesodermCd1ME11halfPkRep2\
type narrowPeak\

wgEncodeLicrHistoneOlfactH3k04me1MAdult8wksC57bl6StdSig	Olfact H3K4m1	bigWig 0.133084 34.513157	Olfactory Bulb 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	173	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Olfactory Bulb 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Olfact H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneOlfactH3k04me1MAdult8wksC57bl6StdSig\
type bigWig 0.133084 34.513157\
viewLimits 0.2:3\

wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep2	Ovary - 2	bigWig 1.000000 1299260.000000	Ovary A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	173	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Ovary A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel Ovary - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=OVARY rep=rep2\
track wgEncodeCshlLongRnaSeqOvaryAdult8wksMinusRawRep2\
type bigWig 1.000000 1299260.000000\

wgEncodeUwDnaseMesodermCd1ME11halfSigRep2	Mesoderm S 2	bigWig 1.000000 80928.000000	Mesoderm DNaseI HS Signal Rep 2 from ENCODE/UW	2	174	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel Mesoderm DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Mesoderm S 2\
subGroups view=Signal age=E11HALF cellType=MESODERM sex=M strain=CD1 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseMesodermCd1ME11halfSigRep2\
type bigWig 1.000000 80928.000000\

wgEncodeLicrHistoneOlfactH3k04me3MAdult8wksC57bl6StdPk	Olfact H3K4m3	broadPeak	Olfactory Bulb 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	174	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Olfactory Bulb 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Olfact H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneOlfactH3k04me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep2	Ovary + 2	bigWig 1.000000 1240022.000000	Ovary A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	174	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Ovary A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Ovary + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=OVARY rep=rep2\
track wgEncodeCshlLongRnaSeqOvaryAdult8wksPlusRawRep2\
type bigWig 1.000000 1240022.000000\

wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep1	mG/ER dPC 24 H 1	broadPeak	mG/ER diffProtC 24 hr DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	175	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER diffProtC 24 hr DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel mG/ER dPC 24 H 1\
subGroups view=Hotspots age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC24H rep=rep1\
track wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneOlfactH3k04me3MAdult8wksC57bl6StdSig	Olfact H3K4m3	bigWig 0.121283 73.194351	Olfactory Bulb 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	175	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Olfactory Bulb 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Olfact H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneOlfactH3k04me3MAdult8wksC57bl6StdSig\
type bigWig 0.121283 73.194351\
viewLimits 0.2:10\

wgEncodeCshlLongRnaSeqOvaryAdult8wksContigs	Ovary C	bed 6 +	Ovary A8 Long RNA-seq Contigs from ENCODE/CSHL	3	175	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Ovary A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs\
shortLabel Ovary C\
subGroups view=Contigs age=ADULT8WKS cellType=OVARY rep=repP\
track wgEncodeCshlLongRnaSeqOvaryAdult8wksContigs\
type bed 6 +\

wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep1	mG/ER dPC 24 P 1	narrowPeak	mG/ER diffProtC 24 hr DNaseI HS Peaks Rep 1 from ENCODE/UW	3	176	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER diffProtC 24 hr DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel mG/ER dPC 24 P 1\
subGroups view=Peaks age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC24H rep=rep1\
track wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep1\
type narrowPeak\

wgEncodeLicrHistoneOlfactH3k27acMAdult8wksC57bl6StdPk	Olfact H3K27a	broadPeak	Olfactory Bulb 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	176	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Olfactory Bulb 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Olfact H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneOlfactH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqOvaryAdult8wksJunctions	Ovary J	bed 6 +	Ovary A8 Long RNA-seq Junctions from ENCODE/CSHL	0	176	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Ovary A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Ovary J\
subGroups view=SJunctions age=ADULT8WKS cellType=OVARY rep=repP\
track wgEncodeCshlLongRnaSeqOvaryAdult8wksJunctions\
type bed 6 +\

wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep1	mG/ER dPC 24 S 1	bigWig 1.000000 67184.000000	mG/ER diffProtC 24 hr DNaseI HS Signal Rep 1 from ENCODE/UW	2	177	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel mG/ER diffProtC 24 hr DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel mG/ER dPC 24 S 1\
subGroups view=Signal age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC24H rep=rep1\
track wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep1\
type bigWig 1.000000 67184.000000\

wgEncodeLicrHistoneOlfactH3k27acMAdult8wksC57bl6StdSig	Olfact H3K27a	bigWig 0.117609 27.520395	Olfactory Bulb 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	177	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Olfactory Bulb 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Olfact H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneOlfactH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.117609 27.520395\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep1	Placenta Aln 1	bam	Placenta A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	177	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Placenta A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Placenta Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=PLAC rep=rep1\
track wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep1\
type bam\

wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep2	mG/ER dPC 24 H 2	broadPeak	mG/ER diffProtC 24 hr DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	178	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER diffProtC 24 hr DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel mG/ER dPC 24 H 2\
subGroups view=Hotspots age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC24H rep=rep2\
track wgEncodeUwDnaseMgerUknImmortalDiffc24hHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneOlfactInputMAdult8wksC57bl6StdSig	Olfact Input	bigWig 0.102227 41.708450	Olfactory Bulb 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	178	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Olfactory Bulb 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Olfact Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=OLFACT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneOlfactInputMAdult8wksC57bl6StdSig\
type bigWig 0.102227 41.708450\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep1	Placenta - 1	bigWig 1.000000 907082.000000	Placenta A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	178	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Placenta - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=PLAC rep=rep1\
track wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep1\
type bigWig 1.000000 907082.000000\

wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep2	mG/ER dPC 24 P 2	narrowPeak	mG/ER diffProtC 24 hr DNaseI HS Peaks Rep 2 from ENCODE/UW	3	179	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER diffProtC 24 hr DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel mG/ER dPC 24 P 2\
subGroups view=Peaks age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC24H rep=rep2\
track wgEncodeUwDnaseMgerUknImmortalDiffc24hPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep1	Placenta + 1	bigWig 1.000000 1833846.000000	Placenta A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	179	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Placenta + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=PLAC rep=rep1\
track wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep1\
type bigWig 1.000000 1833846.000000\

wgEncodeLicrHistonePlacH3k04me1FAdult8wksC57bl6StdPk	Placenta H3K4m1	broadPeak	Placenta 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	179	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Placenta 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Placenta H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=PLAC control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistonePlacH3k04me1FAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep2	mG/ER dPC 24 S 2	bigWig 1.000000 62131.000000	mG/ER diffProtC 24 hr DNaseI HS Signal Rep 2 from ENCODE/UW	2	180	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel mG/ER diffProtC 24 hr DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel mG/ER dPC 24 S 2\
subGroups view=Signal age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC24H rep=rep2\
track wgEncodeUwDnaseMgerUknImmortalDiffc24hSigRep2\
type bigWig 1.000000 62131.000000\

wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep2	Placenta Aln 2	bam	Placenta A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	180	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Placenta A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Placenta Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=PLAC rep=rep2\
track wgEncodeCshlLongRnaSeqPlacAdult8wksAlnRep2\
type bam\

wgEncodeLicrHistonePlacH3k04me1FAdult8wksC57bl6StdSig	Placenta H3K4m1	bigWig 0.150000 46.540001	Placenta 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	180	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Placenta H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=PLAC control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistonePlacH3k04me1FAdult8wksC57bl6StdSig\
type bigWig 0.150000 46.540001\
viewLimits 0.2:3\

wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep1	mG/ER dPC 48 H 1	broadPeak	mG/ER diffProtC 48 hr DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	181	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER diffProtC 48 hr DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel mG/ER dPC 48 H 1\
subGroups view=Hotspots age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC48H rep=rep1\
track wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep2	Placenta - 2	bigWig 1.000000 930592.000000	Placenta A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	181	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Placenta - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=PLAC rep=rep2\
track wgEncodeCshlLongRnaSeqPlacAdult8wksMinusRawRep2\
type bigWig 1.000000 930592.000000\

wgEncodeLicrHistonePlacH3k04me3FAdult8wksC57bl6StdPk	Placenta H3K4m3	broadPeak	Placenta 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	181	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Placenta 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Placenta H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=PLAC control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistonePlacH3k04me3FAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep1	mG/ER dPC 48 P 1	narrowPeak	mG/ER diffProtC 48 hr DNaseI HS Peaks Rep 1 from ENCODE/UW	3	182	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER diffProtC 48 hr DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel mG/ER dPC 48 P 1\
subGroups view=Peaks age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC48H rep=rep1\
track wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep2	Placenta + 2	bigWig 1.000000 5031153.000000	Placenta A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	182	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Placenta + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=PLAC rep=rep2\
track wgEncodeCshlLongRnaSeqPlacAdult8wksPlusRawRep2\
type bigWig 1.000000 5031153.000000\

wgEncodeLicrHistonePlacH3k04me3FAdult8wksC57bl6StdSig	Placenta H3K4m3	bigWig 0.180000 128.720001	Placenta 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	182	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Placenta H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=PLAC control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistonePlacH3k04me3FAdult8wksC57bl6StdSig\
type bigWig 0.180000 128.720001\
viewLimits 0.2:10\

wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep1	mG/ER dPC 48 S 1	bigWig 1.000000 29826.000000	mG/ER diffProtC 48 hr DNaseI HS Signal Rep 1 from ENCODE/UW	2	183	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel mG/ER diffProtC 48 hr DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel mG/ER dPC 48 S 1\
subGroups view=Signal age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC48H rep=rep1\
track wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep1\
type bigWig 1.000000 29826.000000\

wgEncodeCshlLongRnaSeqPlacAdult8wksContigs	Placenta C	bed 6 +	Placenta A8 Long RNA-seq Contigs from ENCODE/CSHL	3	183	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Placenta A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Placenta C\
subGroups view=Contigs age=ADULT8WKS cellType=PLAC rep=repP\
track wgEncodeCshlLongRnaSeqPlacAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistonePlacH3k27acFAdult8wksC57bl6StdPk	Placenta H3K27a	broadPeak	Placenta 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	183	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Placenta 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Placenta H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=PLAC control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistonePlacH3k27acFAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep2	mG/ER dPC 48 H 2	broadPeak	mG/ER diffProtC 48 hr DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	184	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER diffProtC 48 hr DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel mG/ER dPC 48 H 2\
subGroups view=Hotspots age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC48H rep=rep2\
track wgEncodeUwDnaseMgerUknImmortalDiffc48hHotspotsRep2\
type broadPeak\

wgEncodeLicrHistonePlacH3k27acFAdult8wksC57bl6StdSig	Placenta H3K27a	bigWig 0.130000 51.709999	Placenta 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	184	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Placenta H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=PLAC control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistonePlacH3k27acFAdult8wksC57bl6StdSig\
type bigWig 0.130000 51.709999\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqPlacAdult8wksJunctions	Placenta J	bed 6 +	Placenta A8 Long RNA-seq Junctions from ENCODE/CSHL	0	184	153	38	0	204	146	127	0	0	0				regulation	1	color 153,38,0\
longLabel Placenta A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Placenta J\
subGroups view=SJunctions age=ADULT8WKS cellType=PLAC rep=repP\
track wgEncodeCshlLongRnaSeqPlacAdult8wksJunctions\
type bed 6 +\

wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep2	mG/ER dPC 48 P 2	narrowPeak	mG/ER diffProtC 48 hr DNaseI HS Peaks Rep 2 from ENCODE/UW	3	185	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER diffProtC 48 hr DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel mG/ER dPC 48 P 2\
subGroups view=Peaks age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC48H rep=rep2\
track wgEncodeUwDnaseMgerUknImmortalDiffc48hPkRep2\
type narrowPeak\

wgEncodeLicrHistonePlacInputFAdult8wksC57bl6StdSig	Placenta Input	bigWig 0.120000 60.020000	Placenta 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	185	153	38	0	204	146	127	0	0	0				regulation	0	color 153,38,0\
longLabel Placenta 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Placenta Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=PLAC control=STD sex=F strain=C57BL6\
track wgEncodeLicrHistonePlacInputFAdult8wksC57bl6StdSig\
type bigWig 0.120000 60.020000\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep1V2	SmInt Aln 1	bam color 230,159,0 # subId=7759 dateSubmitted=2012-07-29	Small Intestine A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	185	0	0	0	127	127	127	0	0	0				regulation	1	longLabel Small Intestine A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel SmInt Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=SMINT rep=rep1\
track wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep1V2\
type bam color 230,159,0 # subId=7759 dateSubmitted=2012-07-29\

wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep2	mG/ER dPC 48 S 2	bigWig 1.000000 53370.000000	mG/ER diffProtC 48 hr DNaseI HS Signal Rep 2 from ENCODE/UW	2	186	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel mG/ER diffProtC 48 hr DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel mG/ER dPC 48 S 2\
subGroups view=Signal age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=DIFFC48H rep=rep2\
track wgEncodeUwDnaseMgerUknImmortalDiffc48hSigRep2\
type bigWig 1.000000 53370.000000\

wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep1	SmInt - 1	bigWig 1.000000 1662167.000000	Small Intestine A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	186	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel SmInt - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=SMINT rep=rep1\
track wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep1\
type bigWig 1.000000 1662167.000000\

wgEncodeLicrHistoneSmintH3k04me1MAdult8wksC57bl6StdPk	SmInt H3K4m1	broadPeak	Small Intestine 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	186	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel SmInt H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k04me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseMgerUknImmortalHotspotsRep1	mG/ER H 1	broadPeak	mG/ER DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	187	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel mG/ER H 1\
subGroups view=Hotspots age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=zNONE rep=rep1\
track wgEncodeUwDnaseMgerUknImmortalHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep1	SmInt + 1	bigWig 1.000000 3416337.000000	Small Intestine A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	187	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel SmInt + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=SMINT rep=rep1\
track wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep1\
type bigWig 1.000000 3416337.000000\

wgEncodeLicrHistoneSmintH3k04me1MAdult8wksC57bl6StdSig	SmInt H3K4m1	bigWig 0.150000 54.160000	Small Intestine 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	187	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel SmInt H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k04me1MAdult8wksC57bl6StdSig\
type bigWig 0.150000 54.160000\
viewLimits 0.2:3\

wgEncodeUwDnaseMgerUknImmortalPkRep1	mG/ER P 1	narrowPeak	mG/ER DNaseI HS Peaks Rep 1 from ENCODE/UW	3	188	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel mG/ER P 1\
subGroups view=Peaks age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=zNONE rep=rep1\
track wgEncodeUwDnaseMgerUknImmortalPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep2V2	SmInt Aln 2	bam	Small Intestine A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	188	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel SmInt Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=SMINT rep=rep2\
track wgEncodeCshlLongRnaSeqSmintAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistoneSmintH3k04me3MAdult8wksC57bl6StdPk	SmInt H3K4m3	broadPeak	Small Intestine 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	188	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel SmInt H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k04me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseMgerUknImmortalSigRep1	mG/ER S 1	bigWig 1.000000 51430.000000	mG/ER DNaseI HS Signal Rep 1 from ENCODE/UW	2	189	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel mG/ER DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel mG/ER S 1\
subGroups view=Signal age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=zNONE rep=rep1\
track wgEncodeUwDnaseMgerUknImmortalSigRep1\
type bigWig 1.000000 51430.000000\

wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep2	SmInt - 2	bigWig 1.000000 492337.000000	Small Intestine A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	189	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel SmInt - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=SMINT rep=rep2\
track wgEncodeCshlLongRnaSeqSmintAdult8wksMinusRawRep2\
type bigWig 1.000000 492337.000000\

wgEncodeLicrHistoneSmintH3k04me3MAdult8wksC57bl6StdSig	SmInt H3K4m3	bigWig 0.130000 74.949997	Small Intestine 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	189	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel SmInt H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k04me3MAdult8wksC57bl6StdSig\
type bigWig 0.130000 74.949997\
viewLimits 0.2:10\

wgEncodeUwDnaseMgerUknImmortalHotspotsRep2	mG/ER H 2	broadPeak	mG/ER DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	190	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel mG/ER H 2\
subGroups view=Hotspots age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=zNONE rep=rep2\
track wgEncodeUwDnaseMgerUknImmortalHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep2	SmInt + 2	bigWig 1.000000 1357587.000000	Small Intestine A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	190	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel SmInt + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=SMINT rep=rep2\
track wgEncodeCshlLongRnaSeqSmintAdult8wksPlusRawRep2\
type bigWig 1.000000 1357587.000000\

wgEncodeLicrHistoneSmintH3k27acMAdult8wksC57bl6StdPk	SmInt H3K27a	broadPeak	Small Intestine 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	190	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel SmInt H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseMgerUknImmortalPkRep2	mG/ER P 2	narrowPeak	mG/ER DNaseI HS Peaks Rep 2 from ENCODE/UW	3	191	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel mG/ER DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel mG/ER P 2\
subGroups view=Peaks age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=zNONE rep=rep2\
track wgEncodeUwDnaseMgerUknImmortalPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqSmintAdult8wksContigs	SmInt C	bed 6 +	Small Intestine A8 Long RNA-seq Contigs from ENCODE/CSHL	3	191	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel SmInt C\
subGroups view=Contigs age=ADULT8WKS cellType=SMINT rep=repP\
track wgEncodeCshlLongRnaSeqSmintAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneSmintH3k27acMAdult8wksC57bl6StdSig	SmInt H3K27a	bigWig 0.120000 35.220001	Small Intestine 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	191	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel SmInt H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.120000 35.220001\
viewLimits 0.2:5\

wgEncodeUwDnaseMgerUknImmortalSigRep2	mG/ER S 2	bigWig 1.000000 83865.000000	mG/ER DNaseI HS Signal Rep 2 from ENCODE/UW	2	192	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel mG/ER DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel mG/ER S 2\
subGroups view=Signal age=IMMORTAL cellType=MGER sex=M strain=UKN treatment=zNONE rep=rep2\
track wgEncodeUwDnaseMgerUknImmortalSigRep2\
type bigWig 1.000000 83865.000000\

wgEncodeLicrHistoneSmintH3k27me3MAdult8wksC57bl6StdPk	SmInt H3K27m3	broadPeak	Small Intestine 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	192	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel SmInt H3K27m3\
subGroups view=Peaks age=A1DLT8W factor=H3K27ME3 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k27me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqSmintAdult8wksJunctions	SmInt J	bed 6 +	Small Intestine A8 Long RNA-seq Junctions from ENCODE/CSHL	0	192	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel SmInt J\
subGroups view=SJunctions age=ADULT8WKS cellType=SMINT rep=repP\
track wgEncodeCshlLongRnaSeqSmintAdult8wksJunctions\
type bed 6 +\

wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep1	NIH-3T3 H 1	broadPeak	NIH-3T3 DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	193	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel NIH-3T3 DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel NIH-3T3 H 1\
subGroups view=Hotspots age=IMMORTAL cellType=NIH3T3 sex=M strain=NIHS rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneSmintH3k27me3MAdult8wksC57bl6StdSig	SmInt H3K27m3	bigWig 0.120000 51.099998	Small Intestine 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	193	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel SmInt H3K27m3\
subGroups view=Signal age=A1DLT8W factor=H3K27ME3 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k27me3MAdult8wksC57bl6StdSig\
type bigWig 0.120000 51.099998\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep1V2	Spleen Aln 1	bam	Spleen A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	193	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Spleen Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=SPLEEN rep=rep1\
track wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep1V2\
type bam\

wgEncodeUwDnaseNih3t3NihsMImmortalPkRep1	NIH-3T3 P 1	narrowPeak	NIH-3T3 DNaseI HS Peaks Rep 1 from ENCODE/UW	3	194	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel NIH-3T3 DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel NIH-3T3 P 1\
subGroups view=Peaks age=IMMORTAL cellType=NIH3T3 sex=M strain=NIHS rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseNih3t3NihsMImmortalPkRep1\
type narrowPeak\

wgEncodeLicrHistoneSmintH3k36me3MAdult8wksC57bl6StdPk	SmInt H3K36m3	broadPeak	Small Intestine 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	194	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Small Intestine 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel SmInt H3K36m3\
subGroups view=Peaks age=A1DLT8W factor=H3K36ME3 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k36me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep1	Spleen - 1	bigWig 1.000000 1080439.000000	Spleen A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	194	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel Spleen - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=SPLEEN rep=rep1\
track wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep1\
type bigWig 1.000000 1080439.000000\

wgEncodeUwDnaseNih3t3NihsMImmortalSigRep1	NIH-3T3 S 1	bigWig 1.000000 55535.000000	NIH-3T3 DNaseI HS Signal Rep 1 from ENCODE/UW	2	195	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel NIH-3T3 S 1\
subGroups view=Signal age=IMMORTAL cellType=NIH3T3 sex=M strain=NIHS rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseNih3t3NihsMImmortalSigRep1\
type bigWig 1.000000 55535.000000\

wgEncodeLicrHistoneSmintH3k36me3MAdult8wksC57bl6StdSig	SmInt H3K36m3	bigWig 0.120000 19.320000	Small Intestine 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	195	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel SmInt H3K36m3\
subGroups view=Signal age=A1DLT8W factor=H3K36ME3 cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintH3k36me3MAdult8wksC57bl6StdSig\
type bigWig 0.120000 19.320000\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep1	Spleen + 1	bigWig 1.000000 3071679.000000	Spleen A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	195	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Spleen + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=SPLEEN rep=rep1\
track wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep1\
type bigWig 1.000000 3071679.000000\

wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep2	NIH-3T3 H 2	broadPeak	NIH-3T3 DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	196	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel NIH-3T3 DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel NIH-3T3 H 2\
subGroups view=Hotspots age=IMMORTAL cellType=NIH3T3 sex=M strain=NIHS rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseNih3t3NihsMImmortalHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneSmintInputMAdult8wksC57bl6StdSig	SmInt Input	bigWig 0.110000 33.189999	Small Intestine 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	196	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Small Intestine 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel SmInt Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=SMINT control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSmintInputMAdult8wksC57bl6StdSig\
type bigWig 0.110000 33.189999\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep2V2	Spleen Aln 2	bam	Spleen A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	196	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Spleen Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=SPLEEN rep=rep2\
track wgEncodeCshlLongRnaSeqSplAdult8wksAlnRep2V2\
type bam\

wgEncodeUwDnaseNih3t3NihsMImmortalPkRep2	NIH-3T3 P 2	narrowPeak	NIH-3T3 DNaseI HS Peaks Rep 2 from ENCODE/UW	3	197	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel NIH-3T3 DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel NIH-3T3 P 2\
subGroups view=Peaks age=IMMORTAL cellType=NIH3T3 sex=M strain=NIHS rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseNih3t3NihsMImmortalPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep2	Spleen - 2	bigWig 1.000000 2205882.000000	Spleen A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	197	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel Spleen - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=SPLEEN rep=rep2\
track wgEncodeCshlLongRnaSeqSpleenAdult8wksMinusRawRep2\
type bigWig 1.000000 2205882.000000\

wgEncodeLicrHistoneSpleenH3k4me1MAdult8wksC57bl6StdPk	Spleen H3K4m1	broadPeak	Spleen 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	197	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Spleen H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k4me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseNih3t3NihsMImmortalSigRep2	NIH-3T3 S 2	bigWig 1.000000 34373.000000	NIH-3T3 DNaseI HS Signal Rep 2 from ENCODE/UW	2	198	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel NIH-3T3 DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel NIH-3T3 S 2\
subGroups view=Signal age=IMMORTAL cellType=NIH3T3 sex=M strain=NIHS rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseNih3t3NihsMImmortalSigRep2\
type bigWig 1.000000 34373.000000\

wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep2	Spleen + 2	bigWig 1.000000 5738738.000000	Spleen A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	198	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Spleen + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=SPLEEN rep=rep2\
track wgEncodeCshlLongRnaSeqSpleenAdult8wksPlusRawRep2\
type bigWig 1.000000 5738738.000000\

wgEncodeLicrHistoneSpleenH3k4me1MAdult8wksC57bl6StdSig	Spleen H3K4m1	bigWig 0.140000 55.639999	Spleen 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	198	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Spleen H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k4me1MAdult8wksC57bl6StdSig\
type bigWig 0.140000 55.639999\
viewLimits 0.2:3\

wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep1	Patski H 1	broadPeak	Patski DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	199	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Patski DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Patski H 1\
subGroups view=Hotspots age=IMMORTAL cellType=PATSKI sex=M strain=SPBL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqSpleenAdult8wksContigs	Spleen C	bed 6 +	Spleen A8 Long RNA-seq Contigs from ENCODE/CSHL	3	199	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs\
shortLabel Spleen C\
subGroups view=Contigs age=ADULT8WKS cellType=SPLEEN rep=repP\
track wgEncodeCshlLongRnaSeqSpleenAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneSpleenH3k4me3MAdult8wksC57bl6StdPk	Spleen H3K4m3	broadPeak	Spleen 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	199	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Spleen H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k4me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnasePatskiSpbl6MImmortalPkRep1	Patski P 1	narrowPeak	Patski DNaseI HS Peaks Rep 1 from ENCODE/UW	3	200	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Patski DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Patski P 1\
subGroups view=Peaks age=IMMORTAL cellType=PATSKI sex=M strain=SPBL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnasePatskiSpbl6MImmortalPkRep1\
type narrowPeak\

wgEncodeLicrHistoneSpleenH3k4me3MAdult8wksC57bl6StdSig	Spleen H3K4m3	bigWig 0.160000 65.190002	Spleen 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	200	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Spleen H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k4me3MAdult8wksC57bl6StdSig\
type bigWig 0.160000 65.190002\
viewLimits 0.2:10\

wgEncodeCshlLongRnaSeqSpleenAdult8wksJunctions	Spleen J	bed 6 +	Spleen A8 Long RNA-seq Junctions from ENCODE/CSHL	0	200	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Spleen J\
subGroups view=SJunctions age=ADULT8WKS cellType=SPLEEN rep=repP\
track wgEncodeCshlLongRnaSeqSpleenAdult8wksJunctions\
type bed 6 +\

wgEncodeUwDnasePatskiSpbl6MImmortalSigRep1	Patski S 1	bigWig 1.000000 101941.000000	Patski DNaseI HS Signal Rep 1 from ENCODE/UW	2	201	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Patski DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Patski S 1\
subGroups view=Signal age=IMMORTAL cellType=PATSKI sex=M strain=SPBL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnasePatskiSpbl6MImmortalSigRep1\
type bigWig 1.000000 101941.000000\

wgEncodeLicrHistoneSpleenH3k27acMAdult8wksC57bl6StdPk	Spleen H3K27a	broadPeak	Spleen 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	201	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Spleen H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep1V2	Stomach Aln 1	bam	Stomach A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	201	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Stomach A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Stomach Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=STOM rep=rep1\
track wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep1V2\
type bam\

wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep2	Patski H 2	broadPeak	Patski DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	202	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Patski DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Patski H 2\
subGroups view=Hotspots age=IMMORTAL cellType=PATSKI sex=M strain=SPBL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnasePatskiSpbl6MImmortalHotspotsRep2\
type broadPeak\

wgEncodeLicrHistoneSpleenH3k27acMAdult8wksC57bl6StdSig	Spleen H3K27a	bigWig 0.120000 46.990002	Spleen 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	202	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Spleen H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.120000 46.990002\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep1	Stomach - 1	bigWig 1.000000 3101357.000000	Stomach A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	202	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Stomach A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Stomach - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=STOM rep=rep1\
track wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep1\
type bigWig 1.000000 3101357.000000\

wgEncodeUwDnasePatskiSpbl6MImmortalPkRep2	Patski P 2	narrowPeak	Patski DNaseI HS Peaks Rep 2 from ENCODE/UW	3	203	204	121	167	229	188	211	0	0	0				regulation	1	color 204,121,167\
longLabel Patski DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Patski P 2\
subGroups view=Peaks age=IMMORTAL cellType=PATSKI sex=M strain=SPBL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnasePatskiSpbl6MImmortalPkRep2\
type narrowPeak\

wgEncodeLicrHistoneSpleenH3k27me3MAdlt8wC57bl6StdPk	Spleen H3K27m3	broadPeak	Spleen 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	203	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Spleen H3K27m3\
subGroups view=Peaks age=A1DLT8W factor=H3K27ME3 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k27me3MAdlt8wC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep1	Stomach + 1	bigWig 1.000000 2267153.000000	Stomach A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	203	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Stomach A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Stomach + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=STOM rep=rep1\
track wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep1\
type bigWig 1.000000 2267153.000000\

wgEncodeUwDnasePatskiSpbl6MImmortalSigRep2	Patski S 2	bigWig 1.000000 86679.000000	Patski DNaseI HS Signal Rep 2 from ENCODE/UW	2	204	204	121	167	229	188	211	0	0	0				regulation	0	color 204,121,167\
longLabel Patski DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Patski S 2\
subGroups view=Signal age=IMMORTAL cellType=PATSKI sex=M strain=SPBL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnasePatskiSpbl6MImmortalSigRep2\
type bigWig 1.000000 86679.000000\

wgEncodeLicrHistoneSpleenH3k27me3MAdlt8wC57bl6StdSig	Spleen H3K27m3	bigWig 0.120000 42.320000	Spleen 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	204	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Spleen H3K27m3\
subGroups view=Signal age=A1DLT8W factor=H3K27ME3 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k27me3MAdlt8wC57bl6StdSig\
type bigWig 0.120000 42.320000\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep2V2	Stomach Aln 2	bam	Stomach A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	204	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Stomach A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Stomach Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=STOM rep=rep2\
track wgEncodeCshlLongRnaSeqStomAdult8wksAlnRep2V2\
type bam\

wgEncodeUwDnaseRetinaC57bl6MAdult1wksHotspotsRep1	Retina A1w H 1	broadPeak	Retina Adult 1 week DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	205	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Retina Adult 1 week DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Retina A1w H 1\
subGroups view=Hotspots age=ADULT1WKS cellType=RETINA sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseRetinaC57bl6MAdult1wksHotspotsRep1\
type broadPeak\

wgEncodeLicrHistoneSpleenH3k36me3MAdult8wksC57bl6StdPk	Spleen H3K36m3	broadPeak	Spleen 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	205	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Spleen H3K36m3\
subGroups view=Peaks age=A1DLT8W factor=H3K36ME3 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k36me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep2	Stomach - 2	bigWig 1.000000 5462174.000000	Stomach A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	205	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Stomach A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Stomach - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=STOM rep=rep2\
track wgEncodeCshlLongRnaSeqStomAdult8wksMinusRawRep2\
type bigWig 1.000000 5462174.000000\

wgEncodeUwDnaseRetinaC57bl6MAdult1wksPkRep1	Retina A1w P 1	narrowPeak	Retina Adult 1 week DNaseI HS Peaks Rep 1 from ENCODE/UW	3	206	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Retina Adult 1 week DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Retina A1w P 1\
subGroups view=Peaks age=ADULT1WKS cellType=RETINA sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseRetinaC57bl6MAdult1wksPkRep1\
type narrowPeak\

wgEncodeLicrHistoneSpleenH3k36me3MAdult8wksC57bl6StdSig	Spleen H3K36m3	bigWig 0.120000 18.340000	Spleen 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	206	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Spleen H3K36m3\
subGroups view=Signal age=A1DLT8W factor=H3K36ME3 cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenH3k36me3MAdult8wksC57bl6StdSig\
type bigWig 0.120000 18.340000\
viewLimits 0.2:2\

wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep2	Stomach + 2	bigWig 1.000000 4021214.000000	Stomach A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	206	230	159	0	242	207	127	0	0	0				regulation	0	color 230,159,0\
longLabel Stomach A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Stomach + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=STOM rep=rep2\
track wgEncodeCshlLongRnaSeqStomAdult8wksPlusRawRep2\
type bigWig 1.000000 4021214.000000\

wgEncodeUwDnaseRetinaC57bl6MAdult1wksSigRep1	Retina A1w S 1	bigWig 1.000000 47303.000000	Retina Adult 1 week DNaseI HS Signal Rep 1 from ENCODE/UW	2	207	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Retina Adult 1 week DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Retina A1w S 1\
subGroups view=Signal age=ADULT1WKS cellType=RETINA sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseRetinaC57bl6MAdult1wksSigRep1\
type bigWig 1.000000 47303.000000\

wgEncodeLicrHistoneSpleenInputMAdult8wksC57bl6StdSig	Spleen Input	bigWig 0.130000 31.219999	Spleen 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	207	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Spleen Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=SPLEEN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneSpleenInputMAdult8wksC57bl6StdSig\
type bigWig 0.130000 31.219999\
viewLimits 0.2:5\

wgEncodeCshlLongRnaSeqStomAdult8wksContigs	Stomach C	bed 6 +	Stomach A8 Long RNA-seq Contigs from ENCODE/CSHL	3	207	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Stomach A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Stomach C\
subGroups view=Contigs age=ADULT8WKS cellType=STOM rep=repP\
track wgEncodeCshlLongRnaSeqStomAdult8wksContigs\
type bed 6 +\

wgEncodeUwDnaseRetinaC57bl6MAdult8wksHotspotsRep1	Retina A8w H 1	broadPeak	Retina Adult 8 Weeks DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	208	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Retina Adult 8 Weeks DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Retina A8w H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=RETINA sex=M strain=C57BL6 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseRetinaC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqStomAdult8wksJunctions	Stomach J	bed 6 +	Stomach A8 Long RNA-seq Junctions from ENCODE/CSHL	0	208	230	159	0	242	207	127	0	0	0				regulation	1	color 230,159,0\
longLabel Stomach A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Stomach J\
subGroups view=SJunctions age=ADULT8WKS cellType=STOM rep=repP\
track wgEncodeCshlLongRnaSeqStomAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneTestisH3k04me1MAdult8wksC57bl6StdPk	Testis H3K4m1	broadPeak	Testis 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	208	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis 8w H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Testis H3K4m1\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME1 cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneTestisH3k04me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseRetinaC57bl6MAdult8wksPkRep1	Retina A8w P 1	narrowPeak	Retina Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW	3	209	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Retina Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Retina A8w P 1\
subGroups view=Peaks age=ADULT8WKS cellType=RETINA sex=M strain=C57BL6 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseRetinaC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep1V2	SubcFatPad Aln 1	bam	Subcutaneous Fat Pad A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	209	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Subcutaneous Fat Pad A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel SubcFatPad Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=SUFAT rep=rep1\
track wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep1V2\
type bam\

wgEncodeLicrHistoneTestisH3k04me1MAdult8wksC57bl6StdSig	Testis H3K4m1	bigWig 0.120000 62.349998	Testis 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	209	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Testis H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneTestisH3k04me1MAdult8wksC57bl6StdSig\
type bigWig 0.120000 62.349998\
viewLimits 0.2:3\

wgEncodeUwDnaseRetinaC57bl6MAdult8wksSigRep1	Retina A8w S 1	bigWig 1.000000 58938.000000	Retina Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW	2	210	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Retina Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Retina A8w S 1\
subGroups view=Signal age=ADULT8WKS cellType=RETINA sex=M strain=C57BL6 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseRetinaC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 58938.000000\

wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep1	SubcFatPad - 1	bigWig 1.000000 280620.000000	Subcutaneous Fat Pad A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	210	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Subcutaneous Fat Pad A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel SubcFatPad - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=SUFAT rep=rep1\
track wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep1\
type bigWig 1.000000 280620.000000\

wgEncodeLicrHistoneTestisH3k04me3MAdult8wksC57bl6StdPk	Testis H3K4m3	broadPeak	Testis 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	210	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Testis H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneTestisH3k04me3MAdult8wksC57bl6StdPk\
type broadPeak\

chainNetRn4	Rat Chain/Net	bed 3	Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments	0	210.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of rat (Nov. 2004 (Baylor 3.4/rn4)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
rat and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
rat assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best rat/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The rat sequence used in this annotation is from\
the Nov. 2004 (Baylor 3.4/rn4) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the rat/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single rat chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>56</TD><TD>-109</TD><TD>-45</TD><TD>-137</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-109</TD><TD>100</TD><TD>-103</TD><TD>-45</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-45</TD><TD>-103</TD><TD>100</TD><TD>-109</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-137</TD><TD>-45</TD><TD>-109</TD><TD>56</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
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color 0,0,0\
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spectrum on\
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track chainNetRn4\
type bed 3\
visibility hide\

chainNetRn4Viewchain	Chain	bed 3	Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments	3	210.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments\
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chainNetRn4Viewnet	Net	bed 3	Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments	2	210.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Rat (Nov. 2004 (Baylor 3.4/rn4)), Chain and Net Alignments\
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visibility full\

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longLabel Retina Newborn 1 Day DNaseI HS Hotspots Rep 1 from ENCODE/UW\
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wgEncodeCshlLongRnaSeqSfatAdult8wksPlusRawRep1	SubcFatPad + 1	bigWig 1.000000 596899.000000	Subcutaneous Fat Pad A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	211	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Subcutaneous Fat Pad A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
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wgEncodeLicrHistoneTestisH3k04me3MAdult8wksC57bl6StdSig	Testis H3K4m3	bigWig 0.130000 48.570000	Testis 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	211	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
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track wgEncodeLicrHistoneTestisH3k04me3MAdult8wksC57bl6StdSig\
type bigWig 0.130000 48.570000\
viewLimits 0.2:10\

wgEncodeUwDnaseRetinaC57bl6MNew1daysPkRep1	Retina N1d P 1	narrowPeak	Retina Newborn 1 Day DNaseI HS Peaks Rep 1 from ENCODE/UW	3	212	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Retina Newborn 1 Day DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
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track wgEncodeUwDnaseRetinaC57bl6MNew1daysPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep2V2	SubcFatPad Aln 2	bam	Subcutaneous Fat Pad A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	212	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Subcutaneous Fat Pad A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
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subGroups view=Alignments age=ADULT8WKS cellType=SUFAT rep=rep2\
track wgEncodeCshlLongRnaSeqSfatAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistoneTestisH3k27acMAdult8wksC57bl6StdPk	Testis H3K27a	broadPeak	Testis 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	212	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
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subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneTestisH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseRetinaC57bl6MNew1daysSigRep1	Retina N1d S 1	bigWig 1.000000 78231.000000	Retina Newborn 1 Day DNaseI HS Signal Rep 1 from ENCODE/UW	2	213	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Retina Newborn 1 Day DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Retina N1d S 1\
subGroups view=Signal age=NEW1DAYS cellType=RETINA sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseRetinaC57bl6MNew1daysSigRep1\
type bigWig 1.000000 78231.000000\

wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep2	SubcFatPad - 2	bigWig 1.000000 581537.000000	Subcutaneous Fat Pad A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	213	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Subcutaneous Fat Pad A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel SubcFatPad - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=SUFAT rep=rep2\
track wgEncodeCshlLongRnaSeqSfatAdult8wksMinusRawRep2\
type bigWig 1.000000 581537.000000\

wgEncodeLicrHistoneTestisH3k27acMAdult8wksC57bl6StdSig	Testis H3K27a	bigWig 0.130000 55.549999	Testis 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	213	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Testis H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneTestisH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.130000 55.549999\
viewLimits 0.2:5\

wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksHotspotsRep1	Sk Muscle H 1	broadPeak	Skeletal Muscle DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	214	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel Skeletal Muscle DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Sk Muscle H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=SKMUSCLE sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqSfatAdult8wksPlusRawRep2	SubcFatPad + 2	bigWig 1.000000 801696.000000	Subcutaneous Fat Pad A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	214	189	0	157	222	127	206	0	0	0				regulation	0	color 189,0,157\
longLabel Subcutaneous Fat Pad A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel SubcFatPad + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=SUFAT rep=rep2\
track wgEncodeCshlLongRnaSeqSfatAdult8wksPlusRawRep2\
type bigWig 1.000000 801696.000000\

wgEncodeLicrHistoneTestisH3k27me3MAdlt8wC57bl6StdPk	Testis H3K27m3	broadPeak	Testis 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	214	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Testis H3K27m3\
subGroups view=Peaks age=A1DLT8W factor=H3K27ME3 cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneTestisH3k27me3MAdlt8wC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep1	Sk Muscle P 1	narrowPeak	Skeletal Muscle DNaseI HS Peaks Rep 1 from ENCODE/UW	3	215	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
longLabel Skeletal Muscle DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Sk Muscle P 1\
subGroups view=Peaks age=ADULT8WKS cellType=SKMUSCLE sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqSfatAdult8wksContigs	SubcFatPad C	bed 6 +	Subcutaneous Fat Pad A8 Long RNA-seq Contigs from ENCODE/CSHL	3	215	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
longLabel Subcutaneous Fat Pad A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel SubcFatPad C\
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track wgEncodeCshlLongRnaSeqSfatAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneTestisH3k27me3MAdlt8wC57bl6StdSig	Testis H3K27m3	bigWig 0.120000 38.840000	Testis 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	215	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
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subGroups view=Signal age=A1DLT8W factor=H3K27ME3 cellType=TESTIS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneTestisH3k27me3MAdlt8wC57bl6StdSig\
type bigWig 0.120000 38.840000\
viewLimits 0.2:2\

wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep1	Sk Muscle S 1	bigWig 1.000000 75085.000000	Skeletal Muscle DNaseI HS Signal Rep 1 from ENCODE/UW	2	216	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel Skeletal Muscle DNaseI HS Signal Rep 1 from ENCODE/UW\
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track wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 75085.000000\

wgEncodeCshlLongRnaSeqSfatAdult8wksJunctions	SubcFatPad J	bed 6 +	Subcutaneous Fat Pad A8 Long RNA-seq Junctions from ENCODE/CSHL	0	216	189	0	157	222	127	206	0	0	0				regulation	1	color 189,0,157\
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wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksHotspotsRep2	Sk Muscle H 2	broadPeak	Skeletal Muscle DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	217	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
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wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep2	Sk Muscle P 2	narrowPeak	Skeletal Muscle DNaseI HS Peaks Rep 2 from ENCODE/UW	3	218	139	69	19	197	162	137	0	0	0				regulation	1	color 139,69,19\
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track wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksPkRep2\
type narrowPeak\

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shortLabel Testis - 1\
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wgEncodeLicrHistoneTestisInputMAdult8wksC57bl6StdSig	Testis Input	bigWig 0.130000 59.860001	Testis 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	218	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
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wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep2	Sk Muscle S 2	bigWig 1.000000 17517.000000	Skeletal Muscle DNaseI HS Signal Rep 2 from ENCODE/UW	2	219	139	69	19	197	162	137	0	0	0				regulation	0	color 139,69,19\
longLabel Skeletal Muscle DNaseI HS Signal Rep 2 from ENCODE/UW\
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track wgEncodeUwDnaseSkmuscleC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 17517.000000\

wgEncodeCshlLongRnaSeqTestisAdult8wksPlusRawRep1	Testis + 1	bigWig 1.000000 353102.000000	Testis A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	219	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Testis + 1\
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type bigWig 1.000000 353102.000000\

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parent wgEncodeLicrHistoneViewPeaks off\
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track wgEncodeLicrHistoneThymusH3k04me1MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep1	Spleen H 1	broadPeak	Spleen DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	220	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Spleen H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=SPLEEN sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep2V2	Testis Aln 2	bam	Testis A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	220	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Testis Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=TESTIS rep=rep2\
track wgEncodeCshlLongRnaSeqTestisAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistoneThymusH3k04me1MAdult8wksC57bl6StdSig	Thymus H3K4m1	bigWig 0.116118 35.880478	Thymus 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	220	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus 8w H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Thymus H3K4m1\
subGroups view=Signal age=A1DLT8W factor=H3K04ME1 cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusH3k04me1MAdult8wksC57bl6StdSig\
type bigWig 0.116118 35.880478\
viewLimits 0.2:3\

wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep1	Spleen P 1	narrowPeak	Spleen DNaseI HS Peaks Rep 1 from ENCODE/UW	3	221	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Spleen P 1\
subGroups view=Peaks age=ADULT8WKS cellType=SPLEEN sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqTestisAdult8wksMinusRawRep2	Testis - 2	bigWig 1.000000 340729.000000	Testis A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	221	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal\
shortLabel Testis - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=TESTIS rep=rep2\
track wgEncodeCshlLongRnaSeqTestisAdult8wksMinusRawRep2\
type bigWig 1.000000 340729.000000\

wgEncodeLicrHistoneThymusH3k04me3MAdult8wksC57bl6StdPk	Thymus H3K4m3	broadPeak	Thymus 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	221	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus 8w H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Thymus H3K4m3\
subGroups view=Peaks age=A1DLT8W factor=H3K04ME3 cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusH3k04me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep1	Spleen S 1	bigWig 1.000000 64454.000000	Spleen DNaseI HS Signal Rep 1 from ENCODE/UW	2	222	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Spleen S 1\
subGroups view=Signal age=ADULT8WKS cellType=SPLEEN sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 64454.000000\

wgEncodeCshlLongRnaSeqTestisAdult8wksPlusRawRep2	Testis + 2	bigWig 1.000000 554501.000000	Testis A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	222	0	158	115	127	206	185	0	0	0				regulation	0	color 0,158,115\
longLabel Testis A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal\
shortLabel Testis + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=TESTIS rep=rep2\
track wgEncodeCshlLongRnaSeqTestisAdult8wksPlusRawRep2\
type bigWig 1.000000 554501.000000\

wgEncodeLicrHistoneThymusH3k04me3MAdult8wksC57bl6StdSig	Thymus H3K4m3	bigWig 0.121863 86.035187	Thymus 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	222	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus 8w H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Thymus H3K4m3\
subGroups view=Signal age=A1DLT8W factor=H3K04ME3 cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusH3k04me3MAdult8wksC57bl6StdSig\
type bigWig 0.121863 86.035187\
viewLimits 0.2:10\

wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep2	Spleen H 2	broadPeak	Spleen DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	223	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Spleen H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=SPLEEN sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseSpleenC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqTestisAdult8wksContigs	Testis C	bed 6 +	Testis A8 Long RNA-seq Contigs from ENCODE/CSHL	3	223	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs\
shortLabel Testis C\
subGroups view=Contigs age=ADULT8WKS cellType=TESTIS rep=repP\
track wgEncodeCshlLongRnaSeqTestisAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneThymusH3k27acMAdult8wksC57bl6StdPk	Thymus H3K27a	broadPeak	Thymus 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	223	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus 8w H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Thymus H3K27a\
subGroups view=Peaks age=A1DLT8W factor=H3K27AC cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusH3k27acMAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep2	Spleen P 2	narrowPeak	Spleen DNaseI HS Peaks Rep 2 from ENCODE/UW	3	224	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Spleen DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Spleen P 2\
subGroups view=Peaks age=ADULT8WKS cellType=SPLEEN sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseSpleenC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqTestisAdult8wksJunctions	Testis J	bed 6 +	Testis A8 Long RNA-seq Junctions from ENCODE/CSHL	0	224	0	158	115	127	206	185	0	0	0				regulation	1	color 0,158,115\
longLabel Testis A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Testis J\
subGroups view=SJunctions age=ADULT8WKS cellType=TESTIS rep=repP\
track wgEncodeCshlLongRnaSeqTestisAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneThymusH3k27acMAdult8wksC57bl6StdSig	Thymus H3K27a	bigWig 0.103252 37.652710	Thymus 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	224	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus 8w H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Thymus H3K27a\
subGroups view=Signal age=A1DLT8W factor=H3K27AC cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusH3k27acMAdult8wksC57bl6StdSig\
type bigWig 0.103252 37.652710\
viewLimits 0.2:5\

wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep2	Spleen S 2	bigWig 1.000000 124046.000000	Spleen DNaseI HS Signal Rep 2 from ENCODE/UW	2	225	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Spleen DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Spleen S 2\
subGroups view=Signal age=ADULT8WKS cellType=SPLEEN sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseSpleenC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 124046.000000\

wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep1V2	Thymus Aln 1	bam	Thymus A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	225	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus A8 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Thymus Aln 1\
subGroups view=Alignments age=ADULT8WKS cellType=THYMUS rep=rep1\
track wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep1V2\
type bam\

wgEncodeLicrHistoneThymusH3k27me3MAdlt8wC57bl6StdPk	Thymus H3K27m3	broadPeak	Thymus 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	225	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus 8w H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Thymus H3K27m3\
subGroups view=Peaks age=A1DLT8W factor=H3K27ME3 cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusH3k27me3MAdlt8wC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep1	T-Naive H 1	broadPeak	T-Naive DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	226	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel T-Naive DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel T-Naive H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=T1NAIVE sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep1	Thymus - 1	bigWig 1.000000 669286.000000	Thymus A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	226	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus A8 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Thymus - 1\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=THYMUS rep=rep1\
track wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep1\
type bigWig 1.000000 669286.000000\

wgEncodeLicrHistoneThymusH3k27me3MAdlt8wC57bl6StdSig	Thymus H3K27m3	bigWig 0.130000 56.279999	Thymus 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	226	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus 8w H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Thymus H3K27m3\
subGroups view=Signal age=A1DLT8W factor=H3K27ME3 cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusH3k27me3MAdlt8wC57bl6StdSig\
type bigWig 0.130000 56.279999\
viewLimits 0.2:2\

wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep1	T-Naive P 1	narrowPeak	T-Naive DNaseI HS Peaks Rep 1 from ENCODE/UW	3	227	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel T-Naive DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel T-Naive P 1\
subGroups view=Peaks age=ADULT8WKS cellType=T1NAIVE sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep1	Thymus + 1	bigWig 1.000000 1559615.000000	Thymus A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	227	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus A8 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Thymus + 1\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=THYMUS rep=rep1\
track wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep1\
type bigWig 1.000000 1559615.000000\

wgEncodeLicrHistoneThymusH3k36me3MAdult8wksC57bl6StdPk	Thymus H3K36m3	broadPeak	Thymus 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	227	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus 8w H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Thymus H3K36m3\
subGroups view=Peaks age=A1DLT8W factor=H3K36ME3 cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusH3k36me3MAdult8wksC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep1	T-Naive S 1	bigWig 1.000000 87148.000000	T-Naive DNaseI HS Signal Rep 1 from ENCODE/UW	2	228	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel T-Naive DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel T-Naive S 1\
subGroups view=Signal age=ADULT8WKS cellType=T1NAIVE sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 87148.000000\

wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep2V2	Thymus Aln 2	bam	Thymus A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	228	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus A8 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel Thymus Aln 2\
subGroups view=Alignments age=ADULT8WKS cellType=THYMUS rep=rep2\
track wgEncodeCshlLongRnaSeqThymusAdult8wksAlnRep2V2\
type bam\

wgEncodeLicrHistoneThymusH3k36me3MAdult8wksC57bl6StdSig	Thymus H3K36m3	bigWig 0.120000 20.730000	Thymus 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	228	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus 8w H3K36me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Thymus H3K36m3\
subGroups view=Signal age=A1DLT8W factor=H3K36ME3 cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusH3k36me3MAdult8wksC57bl6StdSig\
type bigWig 0.120000 20.730000\
viewLimits 0.2:2\

wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep2	T-Naive H 2	broadPeak	T-Naive DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	229	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel T-Naive DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel T-Naive H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=T1NAIVE sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseTnaiveC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep2	Thymus - 2	bigWig 1.000000 634555.000000	Thymus A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	229	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus A8 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel Thymus - 2\
subGroups view=MinusRawSignal age=ADULT8WKS cellType=THYMUS rep=rep2\
track wgEncodeCshlLongRnaSeqThymusAdult8wksMinusRawRep2\
type bigWig 1.000000 634555.000000\

wgEncodeLicrHistoneThymusInputMAdult8wksC57bl6StdSig	Thymus Input	bigWig 0.122860 69.354546	Thymus 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	229	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus 8w Input Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Thymus Input\
subGroups view=Signal age=A1DLT8W factor=INPUT cellType=THYMUS control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneThymusInputMAdult8wksC57bl6StdSig\
type bigWig 0.122860 69.354546\
viewLimits 0.2:5\

wgEncodeLicrHistoneWbrainH3k04me1UE14halfC57bl6StdPk	Brain H3K4m1	broadPeak	Whole Brain E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	230	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 H3K4me1 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Brain H3K4m1\
subGroups view=Peaks age=E14HALF factor=H3K04ME1 cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k04me1UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep2	T-Naive P 2	narrowPeak	T-Naive DNaseI HS Peaks Rep 2 from ENCODE/UW	3	230	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel T-Naive DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel T-Naive P 2\
subGroups view=Peaks age=ADULT8WKS cellType=T1NAIVE sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseTnaiveC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep2	Thymus + 2	bigWig 1.000000 1366028.000000	Thymus A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	230	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus A8 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel Thymus + 2\
subGroups view=PlusRawSignal age=ADULT8WKS cellType=THYMUS rep=rep2\
track wgEncodeCshlLongRnaSeqThymusAdult8wksPlusRawRep2\
type bigWig 1.000000 1366028.000000\

wgEncodeLicrHistoneWbrainH3k04me1UE14halfC57bl6StdSig	Brain H3K4m1	bigWig 0.110000 18.080000	Whole Brain E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	231	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain E14.5 H3K4me1 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Brain H3K4m1\
subGroups view=Signal age=E14HALF factor=H3K04ME1 cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k04me1UE14halfC57bl6StdSig\
type bigWig 0.110000 18.080000\
viewLimits 0.2:3\

wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep2	T-Naive S 2	bigWig 1.000000 86604.000000	T-Naive DNaseI HS Signal Rep 2 from ENCODE/UW	2	231	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel T-Naive DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel T-Naive S 2\
subGroups view=Signal age=ADULT8WKS cellType=T1NAIVE sex=M strain=C57BL6 rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseTnaiveC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 86604.000000\

wgEncodeCshlLongRnaSeqThymusAdult8wksContigs	Thymus C	bed 6 +	Thymus A8 Long RNA-seq Contigs from ENCODE/CSHL	3	231	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus A8 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel Thymus C\
subGroups view=Contigs age=ADULT8WKS cellType=THYMUS rep=repP\
track wgEncodeCshlLongRnaSeqThymusAdult8wksContigs\
type bed 6 +\

wgEncodeLicrHistoneWbrainH3k04me3UE14halfC57bl6StdPk	Brain H3K4m3	broadPeak	Whole Brain E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	232	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 H3K4me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Brain H3K4m3\
subGroups view=Peaks age=E14HALF factor=H3K04ME3 cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k04me3UE14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep1	THelper-Act H 1	broadPeak	THelper-Activated DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	232	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel THelper-Activated DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel THelper-Act H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=THELPA sex=M strain=C57BL6 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqThymusAdult8wksJunctions	Thymus J	bed 6 +	Thymus A8 Long RNA-seq Junctions from ENCODE/CSHL	0	232	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus A8 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel Thymus J\
subGroups view=SJunctions age=ADULT8WKS cellType=THYMUS rep=repP\
track wgEncodeCshlLongRnaSeqThymusAdult8wksJunctions\
type bed 6 +\

wgEncodeLicrHistoneWbrainH3k04me3UE14halfC57bl6StdSig	Brain H3K4m3	bigWig 0.120000 50.209999	Whole Brain E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	233	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain E14.5 H3K4me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Brain H3K4m3\
subGroups view=Signal age=E14HALF factor=H3K04ME3 cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k04me3UE14halfC57bl6StdSig\
type bigWig 0.120000 50.209999\
viewLimits 0.2:10\

wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep1	THelper-Act P 1	narrowPeak	THelper-Activated DNaseI HS Peaks Rep 1 from ENCODE/UW	3	233	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel THelper-Activated DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel THelper-Act P 1\
subGroups view=Peaks age=ADULT8WKS cellType=THELPA sex=M strain=C57BL6 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep1	WholeBrain Aln 1	bam	Whole Brain E14.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL	0	233	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 Long RNA-seq Alignments Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel WholeBrain Aln 1\
subGroups view=Alignments age=E14HALF cellType=WBRAIN rep=rep1\
track wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep1\
type bam\

wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdPk	Brain H3K9m3	broadPeak	Whole Brain E14.5 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	234	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 H3K9me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Brain H3K9m3\
subGroups view=Peaks age=E14HALF factor=H3K09ME3 cellType=WBRAIN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep1	THelper-Act S 1	bigWig 1.000000 55725.000000	THelper-Activated DNaseI HS Signal Rep 1 from ENCODE/UW	2	234	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel THelper-Activated DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel THelper-Act S 1\
subGroups view=Signal age=ADULT8WKS cellType=THELPA sex=M strain=C57BL6 treatment=zNONE rep=rep1\
track wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 55725.000000\

wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep1	WholeBrain - 1	bigWig 1.000000 484041.000000	Whole Brain E14.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL	2	234	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain E14.5 Long RNA-seq Minus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel WholeBrain - 1\
subGroups view=MinusRawSignal age=E14HALF cellType=WBRAIN rep=rep1\
track wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep1\
type bigWig 1.000000 484041.000000\

wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdSig	Brain H3K9m3	bigWig 0.110000 40.970001	Whole Brain E14.5 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	235	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain E14.5 H3K9me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Brain H3K9m3\
subGroups view=Signal age=E14HALF factor=H3K09ME3 cellType=WBRAIN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k09me3ME14halfC57bl6StdSig\
type bigWig 0.110000 40.970001\
viewLimits 0.2:2\

wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep2	THelper-Act H 2	broadPeak	THelper-Activated DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	235	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel THelper-Activated DNaseI HS Hotspots Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel THelper-Act H 2\
subGroups view=Hotspots age=ADULT8WKS cellType=THELPA sex=M strain=C57BL6 treatment=zNONE rep=rep2\
track wgEncodeUwDnaseThelpaC57bl6MAdult8wksHotspotsRep2\
type broadPeak\

wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep1	WholeBrain + 1	bigWig 1.000000 257245.000000	Whole Brain E14.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL	2	235	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain E14.5 Long RNA-seq Plus Signal Rep 1 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel WholeBrain + 1\
subGroups view=PlusRawSignal age=E14HALF cellType=WBRAIN rep=rep1\
track wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep1\
type bigWig 1.000000 257245.000000\

wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdPk	Brain H3K27a	broadPeak	Whole Brain E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	236	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 H3K27ac Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Brain H3K27a\
subGroups view=Peaks age=E14HALF factor=H3K27AC cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep2	THelper-Act P 2	narrowPeak	THelper-Activated DNaseI HS Peaks Rep 2 from ENCODE/UW	3	236	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel THelper-Activated DNaseI HS Peaks Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel THelper-Act P 2\
subGroups view=Peaks age=ADULT8WKS cellType=THELPA sex=M strain=C57BL6 treatment=zNONE rep=rep2\
track wgEncodeUwDnaseThelpaC57bl6MAdult8wksPkRep2\
type narrowPeak\

wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep2	WholeBrain Aln 2	bam	Whole Brain E14.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL	0	236	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 Long RNA-seq Alignments Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewAlignments off\
shortLabel WholeBrain Aln 2\
subGroups view=Alignments age=E14HALF cellType=WBRAIN rep=rep2\
track wgEncodeCshlLongRnaSeqWbrainE14halfAlnRep2\
type bam\

wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdSig	Brain H3K27a	bigWig 0.110000 47.540001	Whole Brain E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	237	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain E14.5 H3K27ac Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Brain H3K27a\
subGroups view=Signal age=E14HALF factor=H3K27AC cellType=WBRAIN control=STD sex=U strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k27acUE14halfC57bl6StdSig\
type bigWig 0.110000 47.540001\
viewLimits 0.2:5\

wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep2	THelper-Act S 2	bigWig 1.000000 56562.000000	THelper-Activated DNaseI HS Signal Rep 2 from ENCODE/UW	2	237	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel THelper-Activated DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel THelper-Act S 2\
subGroups view=Signal age=ADULT8WKS cellType=THELPA sex=M strain=C57BL6 treatment=zNONE rep=rep2\
track wgEncodeUwDnaseThelpaC57bl6MAdult8wksSigRep2\
type bigWig 1.000000 56562.000000\

wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep2	WholeBrain - 2	bigWig 1.000000 444396.000000	Whole Brain E14.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL	2	237	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain E14.5 Long RNA-seq Minus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewMinusRawSignal off\
shortLabel WholeBrain - 2\
subGroups view=MinusRawSignal age=E14HALF cellType=WBRAIN rep=rep2\
track wgEncodeCshlLongRnaSeqWbrainE14halfMinusRawRep2\
type bigWig 1.000000 444396.000000\

wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdPk	Brain H3K27m3	broadPeak	Whole Brain E14.5 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	238	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 H3K27me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Brain H3K27m3\
subGroups view=Peaks age=E14HALF factor=H3K27ME3 cellType=WBRAIN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseThymusC57bl6MAdult8wksHotspotsRep1	Thymus H 1	broadPeak	Thymus DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	238	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus DNaseI HS Hotspots Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewHotspots off\
shortLabel Thymus H 1\
subGroups view=Hotspots age=ADULT8WKS cellType=THYMUS sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseThymusC57bl6MAdult8wksHotspotsRep1\
type broadPeak\

wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep2	WholeBrain + 2	bigWig 1.000000 957920.000000	Whole Brain E14.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL	2	238	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain E14.5 Long RNA-seq Plus Signal Rep 2 from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewPlusRawSignal off\
shortLabel WholeBrain + 2\
subGroups view=PlusRawSignal age=E14HALF cellType=WBRAIN rep=rep2\
track wgEncodeCshlLongRnaSeqWbrainE14halfPlusRawRep2\
type bigWig 1.000000 957920.000000\

wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdSig	Brain H3K27m3	bigWig 0.130000 58.849998	Whole Brain E14.5 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	239	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain E14.5 H3K27me3 Histone Mods by ChIP-seq Signal from ENCODE/LICR\
parent wgEncodeLicrHistoneViewSignal off\
shortLabel Brain H3K27m3\
subGroups view=Signal age=E14HALF factor=H3K27ME3 cellType=WBRAIN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k27me3ME14halfC57bl6StdSig\
type bigWig 0.130000 58.849998\
viewLimits 0.2:2\

wgEncodeUwDnaseThymusC57bl6MAdult8wksPkRep1	Thymus P 1	narrowPeak	Thymus DNaseI HS Peaks Rep 1 from ENCODE/UW	3	239	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel Thymus DNaseI HS Peaks Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewPeaks off\
shortLabel Thymus P 1\
subGroups view=Peaks age=ADULT8WKS cellType=THYMUS sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseThymusC57bl6MAdult8wksPkRep1\
type narrowPeak\

wgEncodeCshlLongRnaSeqWbrainE14halfContigs	WholeBrain C	bed 6 +	Whole Brain E14.5 Long RNA-seq Contigs from ENCODE/CSHL	3	239	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 Long RNA-seq Contigs from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewContigs off\
shortLabel WholeBrain C\
subGroups view=Contigs age=E14HALF cellType=WBRAIN rep=repP\
track wgEncodeCshlLongRnaSeqWbrainE14halfContigs\
type bed 6 +\

wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdPk	Brain H3K36m3	broadPeak	Whole Brain E14.5 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR	3	240	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 H3K36me3 Histone Mods by ChIP-seq Peaks from ENCODE/LICR\
parent wgEncodeLicrHistoneViewPeaks off\
shortLabel Brain H3K36m3\
subGroups view=Peaks age=E14HALF factor=H3K36ME3 cellType=WBRAIN control=STD sex=M strain=C57BL6\
track wgEncodeLicrHistoneWbrainH3k36me3ME14halfC57bl6StdPk\
type broadPeak\

wgEncodeUwDnaseThymusC57bl6MAdult8wksSigRep1	Thymus S 1	bigWig 1.000000 52662.000000	Thymus DNaseI HS Signal Rep 1 from ENCODE/UW	2	240	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel Thymus DNaseI HS Signal Rep 1 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel Thymus S 1\
subGroups view=Signal age=ADULT8WKS cellType=THYMUS sex=M strain=C57BL6 rep=rep1 treatment=zNONE\
track wgEncodeUwDnaseThymusC57bl6MAdult8wksSigRep1\
type bigWig 1.000000 52662.000000\

wgEncodeCshlLongRnaSeqWbrainE14halfJunctions	WholeBrain J	bed 6 +	Whole Brain E14.5 Long RNA-seq Junctions from ENCODE/CSHL	0	240	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain E14.5 Long RNA-seq Junctions from ENCODE/CSHL\
parent wgEncodeCshlLongRnaSeqViewJunctions off\
shortLabel WholeBrain J\
subGroups view=SJunctions age=E14HALF cellType=WBRAIN rep=repP\
track wgEncodeCshlLongRnaSeqWbrainE14halfJunctions\
type bed 6 +\

chainNetCavPor3	Guinea pig Chain/Net	bed 3	Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments	0	240.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of guinea pig (Feb. 2008 (Broad/cavPor3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
guinea pig and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
guinea pig assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best guinea pig/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The guinea pig sequence used in this annotation is from\
the Feb. 2008 (Broad/cavPor3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the guinea pig/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single guinea pig chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
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html chainNet\
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matrixHeader A, C, G, T\
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priority 240.3\
shortLabel Guinea pig Chain/Net\
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chainNetCavPor3Viewchain	Chain	bed 3	Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments	3	240.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments\
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chainNetCavPor3Viewnet	Net	bed 3	Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments	2	240.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Guinea pig (Feb. 2008 (Broad/cavPor3)), Chain and Net Alignments\
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wgEncodeLicrHistoneWbrainInputUE14halfC57bl6StdSig	Brain Input	bigWig 0.130000 22.879999	Whole Brain E14.5 Input Histone Mods by ChIP-seq Signal from ENCODE/LICR	2	242	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
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wgEncodeUwDnaseTregC57bl6MAdult8wksHotspotsRep1	TReg H 1	broadPeak	TReg DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	244	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
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wgEncodeUwDnaseTregC57bl6MAdult8wksPkRep1	TReg P 1	narrowPeak	TReg DNaseI HS Peaks Rep 1 from ENCODE/UW	3	245	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
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wgEncodeUwDnaseTregC57bl6MAdult8wksSigRep1	TReg S 1	bigWig 1.000000 36553.000000	TReg DNaseI HS Signal Rep 1 from ENCODE/UW	2	246	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
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wgEncodeUwDnaseTregC57bl6MAdult8wksHotspotsRep2	TReg H 2	broadPeak	TReg DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	247	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel TReg DNaseI HS Hotspots Rep 2 from ENCODE/UW\
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type broadPeak\

wgEncodeUwDnaseTregC57bl6MAdult8wksPkRep2	TReg P 2	narrowPeak	TReg DNaseI HS Peaks Rep 2 from ENCODE/UW	3	248	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel TReg DNaseI HS Peaks Rep 2 from ENCODE/UW\
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wgEncodeUwDnaseTregC57bl6MAdult8wksSigRep2	TReg S 2	bigWig 1.000000 79792.000000	TReg DNaseI HS Signal Rep 2 from ENCODE/UW	2	249	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
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wgEncodeUwDnaseTregaC57bl6MAdult8wksHotspotsRep1	TReg-Act H 1	broadPeak	TReg-Activated DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	250	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel TReg-Activated DNaseI HS Hotspots Rep 1 from ENCODE/UW\
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type broadPeak\

wgEncodeUwDnaseTregaC57bl6MAdult8wksPkRep1	TReg-Act P 1	narrowPeak	TReg-Activated DNaseI HS Peaks Rep 1 from ENCODE/UW	3	251	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
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type narrowPeak\

wgEncodeUwDnaseTregaC57bl6MAdult8wksSigRep1	TReg-Act S 1	bigWig 1.000000 95502.000000	TReg-Activated DNaseI HS Signal Rep 1 from ENCODE/UW	2	252	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel TReg-Activated DNaseI HS Signal Rep 1 from ENCODE/UW\
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type bigWig 1.000000 95502.000000\

wgEncodeUwDnaseTregaC57bl6MAdult8wksHotspotsRep2	TReg-Act H 2	broadPeak	TReg-Activated DNaseI HS Hotspots Rep 2 from ENCODE/UW	3	253	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel TReg-Activated DNaseI HS Hotspots Rep 2 from ENCODE/UW\
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type broadPeak\

wgEncodeUwDnaseTregaC57bl6MAdult8wksPkRep2	TReg-Act P 2	narrowPeak	TReg-Activated DNaseI HS Peaks Rep 2 from ENCODE/UW	3	254	86	180	233	170	217	244	0	0	0				regulation	1	color 86,180,233\
longLabel TReg-Activated DNaseI HS Peaks Rep 2 from ENCODE/UW\
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wgEncodeUwDnaseTregaC57bl6MAdult8wksSigRep2	TReg-Act S 2	bigWig 1.000000 95707.000000	TReg-Activated DNaseI HS Signal Rep 2 from ENCODE/UW	2	255	86	180	233	170	217	244	0	0	0				regulation	0	color 86,180,233\
longLabel TReg-Activated DNaseI HS Signal Rep 2 from ENCODE/UW\
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wgEncodeUwDnaseWbrainC57bl6MAdult8wksHotspotsRep1	Brain A8w H 1	broadPeak	Whole Brain Adult 8 Weeks DNaseI HS Hotspots Rep 1 from ENCODE/UW	3	256	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
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wgEncodeUwDnaseWbrainC57bl6MAdult8wksPkRep1	Brain A8w P 1	narrowPeak	Whole Brain Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW	3	257	105	105	105	180	180	180	0	0	0				regulation	1	color 105,105,105\
longLabel Whole Brain Adult 8 Weeks DNaseI HS Peaks Rep 1 from ENCODE/UW\
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wgEncodeUwDnaseWbrainC57bl6MAdult8wksSigRep1	Brain A8w S 1	bigWig 1.000000 27364.000000	Whole Brain Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW	2	258	105	105	105	180	180	180	0	0	0				regulation	0	color 105,105,105\
longLabel Whole Brain Adult 8 Weeks DNaseI HS Signal Rep 1 from ENCODE/UW\
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chainNetOryCun2	Rabbit Chain/Net	bed 3	Rabbit (Apr. 2009 (Broad/oryCun2)), Chain and Net Alignments	0	260.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of rabbit (Apr. 2009 (Broad/oryCun2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
rabbit and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
rabbit assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best rabbit/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The rabbit sequence used in this annotation is from\
the Apr. 2009 (Broad/oryCun2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the rabbit/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single rabbit chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
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wgEncodeUwDnaseZhbtc4129olaME0SigRep2	ZhBTc4 S 2	bigWig 1.000000 94703.000000	ZhBTc4 DNaseI HS Signal Rep 2 from ENCODE/UW	2	291	65	105	225	160	180	240	0	0	0				regulation	0	color 65,105,225\
longLabel ZhBTc4 DNaseI HS Signal Rep 2 from ENCODE/UW\
parent wgEncodeUwDnaseViewRawSignal off\
shortLabel ZhBTc4 S 2\
subGroups view=Signal age=E0 cellType=ZHBTC4 sex=M strain=a129OLA rep=rep2 treatment=zNONE\
track wgEncodeUwDnaseZhbtc4129olaME0SigRep2\
type bigWig 1.000000 94703.000000\

laminB1_ES	mouse LaminB1 ESC	wig -5.58 4.62	NKI LaminB1 (DamID of LaminB1 in mouse Embryonic Stem cells, log2-ratio)	0	310	255	165	0	255	210	127	0	0	0			<H2>Overview</H2>\
\
<div class="figure" style="float: right;  width: 439px; border: thin silver solid ; margin: 0 20px\
20px 20px; padding: 20px 10px 10px 10px; text-align: center; font-size: 0.9em; background-color:\
#e9e9e9;"> <img src="../images/laminB1Mm9.png" alt="Nuclear Lamina and Chromosomal Organization in\
Mouse Cells"> <p>Model of chromosome organization in interphase, summarizing the main results\
presented in this paper. Large, discrete chromosomal domains are dynamically associated with the\
nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al.\
2010).</p> </div>\
\
<P>The three-dimensional organization of chromosomes within the nucleus and its dynamics during\
differentiation are largely unknown. To visualize this process in molecular detail, high-resolution\
maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem\
cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into\
terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse\
embryonic fibroblasts were profiled.</P>\
\
<P>This revealed that a basal chromosome architecture present in embryonic stem cells is\
cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal\
differentiation. This remodeling involves both individual transcription units and multi-gene\
regions, and affects many genes that determine cellular identity. Often, genes that move away from\
the lamina are concomitantly activated; many others however remain inactive yet become unlocked for\
activation in a next differentiation step. These results suggest that lamina-genome interactions are\
widely involved in the control of gene expression programs during lineage commitment and terminal\
differentiation.</P>\
\
<h3> NKI mouse LaminB1 ESC track </h3> <P> The mouse LaminB1 ESC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
stem cells. </P>\
\
<h3> NKI mouse LaminB1 NPC track </h3> <P> The mouse LaminB1 NPC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural\
progenitor cells. </P>\
\
<h3> NKI mouse LaminB1 AC track </h3> <P> The mouse LaminB1 AC track shows a high resolution map of\
the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes.\
</P>\
\
<h3> NKI mouse LaminB1 MEF track </h3> <P> The mouse LaminB1 MEF track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
fibroblasts. </P>\
\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for\
the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5  standard deviations.\
</P>\
\
<P> For an example region see genomic location: <a\
href="/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=chr14:92,000,000-96,000,000&refGene=\
pack&laminB1Super=show&laminB1_ES=full&laminB1_AC=full&laminB1_NP=full&laminB1_EF=full">chr14:92,000\
,000-96,000,000</a> (Fig 3A, Peric-Hupkes, Meuleman <EM>et al.</EM>, 2010). </P>\
\
\
<H2>Methods</H2>\
\
<P>The DamID technique was applied to generate high-resolution maps of NL interactions for the\
entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact\
in vivo with a protein of interest. </P>\
\
\
\
\
<P>DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein\
consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was\
introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most\
eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by\
immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique\
methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. <a\
href="https://chromatingenomics.org/damid/">Unfused Dam</a> was used as a reference. The\
data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only.</P>\
\
<P> Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on\
a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize\
unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed\
by quantile normalization across the single channel data of all hybridizations. Replicate arrays\
were averaged. </P>\
\
\
<H2>Verification</H2>\
\
<P> The data are based on two independent biological replicates for each cell type, performed on\
separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1\
associated regions are preferentially located at the nuclear periphery. The array platform, the <A\
HREF="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">raw and normalized\
data</A> have been deposited at the <a href="https://www.ncbi.nlm.nih.gov/geo/">NCBI Gene Expression\
Omnibus (GEO)</a> under accession number <a\
href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">GSE17051</A>. </P>\
\
\
<H2>Credits</H2>\
\
<P> The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van\
Steensel at the <A HREF="https://chromatingenomics.org/" TARGET=_blank>Van Steensel Lab</A>,\
Netherlands Cancer Institute. </P>\
\
\
<H2>References</H2>\
<p>\
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P,\
Kerkhoven RM, van Lohuizen M <em>et al</em>.\
<a href="https://www.sciencedirect.com/science/article/pii/S1097276510003217" target="_blank">\
Molecular maps of the reorganization of genome-nuclear lamina interactions during\
differentiation</a>.\
<em>Mol Cell</em>. 2010 May 28;38(4):603-13.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20513434" target="_blank">20513434</a>\
</p>\
	regulation	0	autoScale Off\
color 255, 165, 0\
group regulation\
html laminB1Mm9\
longLabel NKI LaminB1 (DamID of LaminB1 in mouse Embryonic Stem cells, log2-ratio)\
maxHeightPixels 100:40:11\
priority 310\
shortLabel mouse LaminB1 ESC\
smoothingWindow 2\
spanList 60\
superTrack laminB1Super full\
track laminB1_ES\
type wig -5.58 4.62\
viewLimits -1.5:1.5\
visibility hide\
windowingFunction mean\

chainNetCalJac3	Marmoset Chain/Net	bed 3	Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments	0	310.3	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of marmoset (March 2009 (WUGSC 3.2/calJac3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
marmoset and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
marmoset assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best marmoset/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The marmoset sequence used in this annotation is from\
the March 2009 (WUGSC 3.2/calJac3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the marmoset/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single marmoset chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb calJac3\
priority 310.3\
shortLabel Marmoset Chain/Net\
sortOrder view=+\
subGroup1 view Views chain=Chain net=Net\
track chainNetCalJac3\
type bed 3\
visibility hide\

chainNetCalJac3Viewchain	Chain	bed 3	Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments	3	310.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments\
parent chainNetCalJac3\
shortLabel Chain\
spectrum on\
track chainNetCalJac3Viewchain\
view chain\
visibility pack\

chainNetCalJac3Viewnet	Net	bed 3	Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments	2	310.3	0	0	0	100	50	0	0	0	0				compGeno	1	longLabel Marmoset (March 2009 (WUGSC 3.2/calJac3)), Chain and Net Alignments\
parent chainNetCalJac3\
shortLabel Net\
track chainNetCalJac3Viewnet\
view net\
visibility full\

laminB1_NP	mouse LaminB1 NPC	wig -6.00 4.30	NKI LaminB1 (DamID of LaminB1 in mouse Neural Progenitor cells, log2-ratio)	0	320	0	0	255	127	127	255	0	0	0			<H2>Overview</H2>\
\
<div class="figure" style="float: right;  width: 439px; border: thin silver solid ; margin: 0 20px\
20px 20px; padding: 20px 10px 10px 10px; text-align: center; font-size: 0.9em; background-color:\
#e9e9e9;"> <img src="../images/laminB1Mm9.png" alt="Nuclear Lamina and Chromosomal Organization in\
Mouse Cells"> <p>Model of chromosome organization in interphase, summarizing the main results\
presented in this paper. Large, discrete chromosomal domains are dynamically associated with the\
nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al.\
2010).</p> </div>\
\
<P>The three-dimensional organization of chromosomes within the nucleus and its dynamics during\
differentiation are largely unknown. To visualize this process in molecular detail, high-resolution\
maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem\
cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into\
terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse\
embryonic fibroblasts were profiled.</P>\
\
<P>This revealed that a basal chromosome architecture present in embryonic stem cells is\
cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal\
differentiation. This remodeling involves both individual transcription units and multi-gene\
regions, and affects many genes that determine cellular identity. Often, genes that move away from\
the lamina are concomitantly activated; many others however remain inactive yet become unlocked for\
activation in a next differentiation step. These results suggest that lamina-genome interactions are\
widely involved in the control of gene expression programs during lineage commitment and terminal\
differentiation.</P>\
\
<h3> NKI mouse LaminB1 ESC track </h3> <P> The mouse LaminB1 ESC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
stem cells. </P>\
\
<h3> NKI mouse LaminB1 NPC track </h3> <P> The mouse LaminB1 NPC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural\
progenitor cells. </P>\
\
<h3> NKI mouse LaminB1 AC track </h3> <P> The mouse LaminB1 AC track shows a high resolution map of\
the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes.\
</P>\
\
<h3> NKI mouse LaminB1 MEF track </h3> <P> The mouse LaminB1 MEF track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
fibroblasts. </P>\
\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for\
the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5  standard deviations.\
</P>\
\
<P> For an example region see genomic location: <a\
href="/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=chr14:92,000,000-96,000,000&refGene=\
pack&laminB1Super=show&laminB1_ES=full&laminB1_AC=full&laminB1_NP=full&laminB1_EF=full">chr14:92,000\
,000-96,000,000</a> (Fig 3A, Peric-Hupkes, Meuleman <EM>et al.</EM>, 2010). </P>\
\
\
<H2>Methods</H2>\
\
<P>The DamID technique was applied to generate high-resolution maps of NL interactions for the\
entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact\
in vivo with a protein of interest. </P>\
\
\
\
\
<P>DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein\
consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was\
introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most\
eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by\
immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique\
methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. <a\
href="https://chromatingenomics.org/damid/">Unfused Dam</a> was used as a reference. The\
data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only.</P>\
\
<P> Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on\
a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize\
unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed\
by quantile normalization across the single channel data of all hybridizations. Replicate arrays\
were averaged. </P>\
\
\
<H2>Verification</H2>\
\
<P> The data are based on two independent biological replicates for each cell type, performed on\
separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1\
associated regions are preferentially located at the nuclear periphery. The array platform, the <A\
HREF="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">raw and normalized\
data</A> have been deposited at the <a href="https://www.ncbi.nlm.nih.gov/geo/">NCBI Gene Expression\
Omnibus (GEO)</a> under accession number <a\
href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">GSE17051</A>. </P>\
\
\
<H2>Credits</H2>\
\
<P> The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van\
Steensel at the <A HREF="https://chromatingenomics.org/" TARGET=_blank>Van Steensel Lab</A>,\
Netherlands Cancer Institute. </P>\
\
\
<H2>References</H2>\
<p>\
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P,\
Kerkhoven RM, van Lohuizen M <em>et al</em>.\
<a href="https://www.sciencedirect.com/science/article/pii/S1097276510003217" target="_blank">\
Molecular maps of the reorganization of genome-nuclear lamina interactions during\
differentiation</a>.\
<em>Mol Cell</em>. 2010 May 28;38(4):603-13.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20513434" target="_blank">20513434</a>\
</p>\
	regulation	0	autoScale Off\
color 0,0,255\
group regulation\
html laminB1Mm9\
longLabel NKI LaminB1 (DamID of LaminB1 in mouse Neural Progenitor cells, log2-ratio)\
maxHeightPixels 100:40:11\
priority 320\
shortLabel mouse LaminB1 NPC\
smoothingWindow 2\
spanList 60\
superTrack laminB1Super full\
track laminB1_NP\
type wig -6.00 4.30\
viewLimits -1.5:1.5\
visibility hide\
windowingFunction mean\

chainNetRheMac2	Rhesus Chain/Net	bed 3	Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments	0	320.3	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
rhesus and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
rhesus assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best rhesus/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The rhesus sequence used in this annotation is from\
the Jan. 2006 (MGSC Merged 1.0/rheMac2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the rhesus/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single rhesus chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb rheMac2\
priority 320.3\
shortLabel Rhesus Chain/Net\
sortOrder view=+\
subGroup1 view Views chain=Chain net=Net\
track chainNetRheMac2\
type bed 3\
visibility hide\

chainNetRheMac2Viewchain	Chain	bed 3	Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments	3	320.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments\
parent chainNetRheMac2\
shortLabel Chain\
spectrum on\
track chainNetRheMac2Viewchain\
view chain\
visibility pack\

chainNetRheMac2Viewnet	Net	bed 3	Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments	2	320.3	0	0	0	100	50	0	0	0	0				compGeno	1	longLabel Rhesus (Jan. 2006 (MGSC Merged 1.0/rheMac2)), Chain and Net Alignments\
parent chainNetRheMac2\
shortLabel Net\
track chainNetRheMac2Viewnet\
view net\
visibility full\

laminB1_AC	mouse LaminB1 AC	wig -5.75 4.30	NKI LaminB1 (DamID of LaminB1 in mouse Astrocytes, log2-ratio)	0	330	255	0	255	255	127	255	0	0	0			<H2>Overview</H2>\
\
<div class="figure" style="float: right;  width: 439px; border: thin silver solid ; margin: 0 20px\
20px 20px; padding: 20px 10px 10px 10px; text-align: center; font-size: 0.9em; background-color:\
#e9e9e9;"> <img src="../images/laminB1Mm9.png" alt="Nuclear Lamina and Chromosomal Organization in\
Mouse Cells"> <p>Model of chromosome organization in interphase, summarizing the main results\
presented in this paper. Large, discrete chromosomal domains are dynamically associated with the\
nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al.\
2010).</p> </div>\
\
<P>The three-dimensional organization of chromosomes within the nucleus and its dynamics during\
differentiation are largely unknown. To visualize this process in molecular detail, high-resolution\
maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem\
cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into\
terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse\
embryonic fibroblasts were profiled.</P>\
\
<P>This revealed that a basal chromosome architecture present in embryonic stem cells is\
cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal\
differentiation. This remodeling involves both individual transcription units and multi-gene\
regions, and affects many genes that determine cellular identity. Often, genes that move away from\
the lamina are concomitantly activated; many others however remain inactive yet become unlocked for\
activation in a next differentiation step. These results suggest that lamina-genome interactions are\
widely involved in the control of gene expression programs during lineage commitment and terminal\
differentiation.</P>\
\
<h3> NKI mouse LaminB1 ESC track </h3> <P> The mouse LaminB1 ESC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
stem cells. </P>\
\
<h3> NKI mouse LaminB1 NPC track </h3> <P> The mouse LaminB1 NPC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural\
progenitor cells. </P>\
\
<h3> NKI mouse LaminB1 AC track </h3> <P> The mouse LaminB1 AC track shows a high resolution map of\
the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes.\
</P>\
\
<h3> NKI mouse LaminB1 MEF track </h3> <P> The mouse LaminB1 MEF track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
fibroblasts. </P>\
\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for\
the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5  standard deviations.\
</P>\
\
<P> For an example region see genomic location: <a\
href="/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=chr14:92,000,000-96,000,000&refGene=\
pack&laminB1Super=show&laminB1_ES=full&laminB1_AC=full&laminB1_NP=full&laminB1_EF=full">chr14:92,000\
,000-96,000,000</a> (Fig 3A, Peric-Hupkes, Meuleman <EM>et al.</EM>, 2010). </P>\
\
\
<H2>Methods</H2>\
\
<P>The DamID technique was applied to generate high-resolution maps of NL interactions for the\
entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact\
in vivo with a protein of interest. </P>\
\
\
\
\
<P>DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein\
consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was\
introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most\
eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by\
immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique\
methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. <a\
href="https://chromatingenomics.org/damid/">Unfused Dam</a> was used as a reference. The\
data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only.</P>\
\
<P> Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on\
a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize\
unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed\
by quantile normalization across the single channel data of all hybridizations. Replicate arrays\
were averaged. </P>\
\
\
<H2>Verification</H2>\
\
<P> The data are based on two independent biological replicates for each cell type, performed on\
separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1\
associated regions are preferentially located at the nuclear periphery. The array platform, the <A\
HREF="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">raw and normalized\
data</A> have been deposited at the <a href="https://www.ncbi.nlm.nih.gov/geo/">NCBI Gene Expression\
Omnibus (GEO)</a> under accession number <a\
href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">GSE17051</A>. </P>\
\
\
<H2>Credits</H2>\
\
<P> The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van\
Steensel at the <A HREF="https://chromatingenomics.org/" TARGET=_blank>Van Steensel Lab</A>,\
Netherlands Cancer Institute. </P>\
\
\
<H2>References</H2>\
<p>\
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P,\
Kerkhoven RM, van Lohuizen M <em>et al</em>.\
<a href="https://www.sciencedirect.com/science/article/pii/S1097276510003217" target="_blank">\
Molecular maps of the reorganization of genome-nuclear lamina interactions during\
differentiation</a>.\
<em>Mol Cell</em>. 2010 May 28;38(4):603-13.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20513434" target="_blank">20513434</a>\
</p>\
	regulation	0	autoScale Off\
color 255,0,255\
group regulation\
html laminB1Mm9\
longLabel NKI LaminB1 (DamID of LaminB1 in mouse Astrocytes, log2-ratio)\
maxHeightPixels 100:40:11\
priority 330\
shortLabel mouse LaminB1 AC\
smoothingWindow 2\
spanList 60\
superTrack laminB1Super full\
track laminB1_AC\
type wig -5.75 4.30\
viewLimits -1.5:1.5\
visibility hide\
windowingFunction mean\

chainNetPonAbe2	Orangutan Chain/Net	bed 3	Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments	0	330.3	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
orangutan and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
orangutan assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best orangutan/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The orangutan sequence used in this annotation is from\
the July 2007 (WUGSC 2.0.2/ponAbe2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the orangutan/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single orangutan chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
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chainNetPonAbe2Viewnet	Net	bed 3	Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments	2	330.3	0	0	0	100	50	0	0	0	0				compGeno	1	longLabel Orangutan (July 2007 (WUGSC 2.0.2/ponAbe2)), Chain and Net Alignments\
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laminB1_EF	mouse LaminB1 MEF	wig -5.45 4.93	NKI LaminB1 (DamID of LaminB1 in mouse Embryonic Fibroblasts, log2-ratio)	0	340	0	100	0	127	177	127	0	0	0			<H2>Overview</H2>\
\
<div class="figure" style="float: right;  width: 439px; border: thin silver solid ; margin: 0 20px\
20px 20px; padding: 20px 10px 10px 10px; text-align: center; font-size: 0.9em; background-color:\
#e9e9e9;"> <img src="../images/laminB1Mm9.png" alt="Nuclear Lamina and Chromosomal Organization in\
Mouse Cells"> <p>Model of chromosome organization in interphase, summarizing the main results\
presented in this paper. Large, discrete chromosomal domains are dynamically associated with the\
nuclear lamina (NL), in a manner that is dependent on the cell type (Fig. 7, Peric-Hupkes, et al.\
2010).</p> </div>\
\
<P>The three-dimensional organization of chromosomes within the nucleus and its dynamics during\
differentiation are largely unknown. To visualize this process in molecular detail, high-resolution\
maps of genome-nuclear lamina interactions during subsequent differentiation of mouse embryonic stem\
cells were generated via lineage-committed neural precursor (or, neural progenitor) cells into\
terminally differentiated astrocytes. In addition, genome-nuclear lamina interactions for mouse\
embryonic fibroblasts were profiled.</P>\
\
<P>This revealed that a basal chromosome architecture present in embryonic stem cells is\
cumulatively altered at hundreds of sites during lineage commitment and subsequent terminal\
differentiation. This remodeling involves both individual transcription units and multi-gene\
regions, and affects many genes that determine cellular identity. Often, genes that move away from\
the lamina are concomitantly activated; many others however remain inactive yet become unlocked for\
activation in a next differentiation step. These results suggest that lamina-genome interactions are\
widely involved in the control of gene expression programs during lineage commitment and terminal\
differentiation.</P>\
\
<h3> NKI mouse LaminB1 ESC track </h3> <P> The mouse LaminB1 ESC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
stem cells. </P>\
\
<h3> NKI mouse LaminB1 NPC track </h3> <P> The mouse LaminB1 NPC track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse neural\
progenitor cells. </P>\
\
<h3> NKI mouse LaminB1 AC track </h3> <P> The mouse LaminB1 AC track shows a high resolution map of\
the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse astrocytes.\
</P>\
\
<h3> NKI mouse LaminB1 MEF track </h3> <P> The mouse LaminB1 MEF track shows a high resolution map\
of the interaction sites of the entire genome with Lamin B1 (a key NL component) in mouse embryonic\
fibroblasts. </P>\
\
\
<H2>Display Conventions and Configuration</H2>\
\
<P>The LaminB1 wiggle tracks values range from -6.00 to 4.93. The default vertical viewing range for\
the wiggle track was chosen from -1.5 to 1.5 because this is roughly +/- 1.5  standard deviations.\
</P>\
\
<P> For an example region see genomic location: <a\
href="/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=chr14:92,000,000-96,000,000&refGene=\
pack&laminB1Super=show&laminB1_ES=full&laminB1_AC=full&laminB1_NP=full&laminB1_EF=full">chr14:92,000\
,000-96,000,000</a> (Fig 3A, Peric-Hupkes, Meuleman <EM>et al.</EM>, 2010). </P>\
\
\
<H2>Methods</H2>\
\
<P>The DamID technique was applied to generate high-resolution maps of NL interactions for the\
entire mouse genome. DamID is based on targeted adenine methylation of DNA sequences that interact\
in vivo with a protein of interest. </P>\
\
\
\
\
<P>DamID was performed as described (Peric-Hupkes, et al. 2010). In short, a fusion protein\
consisting of Escherichia coli DNA adenine methyltransferase (Dam) fused to mouse LaminB1 was\
introduced into cultured cells. Dam methylates adenines in the sequence GATC, a mark absent in most\
eukaryotes. Here, the LaminB1-Dam fusion protein incorporates in the nuclear lamina, as verified by\
immunofluorescence staining. Hence, the sequences near the nuclear lamina are marked with a unique\
methylation tag. The adenine methylation pattern was detected with genomic tiling arrays. <a\
href="https://chromatingenomics.org/damid/">Unfused Dam</a> was used as a reference. The\
data shown are the log2-ratio of LaminB1-Dam fusion protein over Dam-only.</P>\
\
<P> Sample labelling and hybridizations were performed as described (Peric-Hupkes, et al. 2010), on\
a custom-designed Nimblegen HD2 array, with a median probe spacing of ~1kbp. All probes recognize\
unique (non-repetitive) sequences. The raw data was log2 transformed and loess normalized, followed\
by quantile normalization across the single channel data of all hybridizations. Replicate arrays\
were averaged. </P>\
\
\
<H2>Verification</H2>\
\
<P> The data are based on two independent biological replicates for each cell type, performed on\
separate days. Fluorescence in situ hybridization microscopy confirmed that most of the LaminB1\
associated regions are preferentially located at the nuclear periphery. The array platform, the <A\
HREF="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">raw and normalized\
data</A> have been deposited at the <a href="https://www.ncbi.nlm.nih.gov/geo/">NCBI Gene Expression\
Omnibus (GEO)</a> under accession number <a\
href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17051" TARGET="_BLANK">GSE17051</A>. </P>\
\
\
<H2>Credits</H2>\
\
<P> The data for this track were generated by Daan Peric-Hupkes, Wouter Meuleman and Bas van\
Steensel at the <A HREF="https://chromatingenomics.org/" TARGET=_blank>Van Steensel Lab</A>,\
Netherlands Cancer Institute. </P>\
\
\
<H2>References</H2>\
<p>\
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Gr&#228;f S, Flicek P,\
Kerkhoven RM, van Lohuizen M <em>et al</em>.\
<a href="https://www.sciencedirect.com/science/article/pii/S1097276510003217" target="_blank">\
Molecular maps of the reorganization of genome-nuclear lamina interactions during\
differentiation</a>.\
<em>Mol Cell</em>. 2010 May 28;38(4):603-13.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20513434" target="_blank">20513434</a>\
</p>\
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chainNetPanTro3	Chimp Chain/Net	bed 3	Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments	0	350.3	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of chimp (Oct. 2010 (CGSC 2.1.3/panTro3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
chimp and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
chimp assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best chimp/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The chimp sequence used in this annotation is from\
the Oct. 2010 (CGSC 2.1.3/panTro3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the chimp/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single chimp chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
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chainLinearGap medium\
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compositeTrack on\
dragAndDrop subTracks\
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chainNetPanTro3Viewchain	Chain	bed 3	Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments	3	350.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments\
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chainNetPanTro3Viewnet	Net	bed 3	Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments	2	350.3	0	0	0	100	50	0	0	0	0				compGeno	1	longLabel Chimp (Oct. 2010 (CGSC 2.1.3/panTro3)), Chain and Net Alignments\
parent chainNetPanTro3\
shortLabel Net\
track chainNetPanTro3Viewnet\
view net\
visibility full\

chainNetHg19	Human Chain/Net	bed 3	Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments	0	360.3	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of human (Feb. 2009 (GRCh37/hg19)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
human and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
human assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best human/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The human sequence used in this annotation is from\
the Feb. 2009 (GRCh37/hg19) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the human/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single human chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb hg19\
priority 360.3\
shortLabel Human Chain/Net\
sortOrder view=+\
subGroup1 view Views chain=Chain net=Net\
track chainNetHg19\
type bed 3\
visibility hide\

chainNetHg19Viewchain	Chain	bed 3	Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments	3	360.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments\
parent chainNetHg19\
shortLabel Chain\
spectrum on\
track chainNetHg19Viewchain\
view chain\
visibility pack\

chainNetHg19Viewnet	Net	bed 3	Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments	2	360.3	0	0	0	100	50	0	0	0	0				compGeno	1	longLabel Human (Feb. 2009 (GRCh37/hg19)), Chain and Net Alignments\
parent chainNetHg19\
shortLabel Net\
track chainNetHg19Viewnet\
view net\
visibility full\

chainNetAilMel1	Panda Chain/Net	bed 3	Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments	0	405.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
panda and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
panda assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best panda/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The panda sequence used in this annotation is from\
the Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the panda/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single panda chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb ailMel1\
priority 405.3\
shortLabel Panda Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetAilMel1\
type bed 3\
visibility hide\

chainNetAilMel1Viewchain	Chain	bed 3	Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments	3	405.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments\
parent chainNetAilMel1\
shortLabel Chain\
spectrum on\
track chainNetAilMel1Viewchain\
view chain\
visibility pack\

chainNetAilMel1Viewnet	Net	bed 3	Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments	2	405.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Panda (Dec. 2009 (BGI-Shenzhen 1.0/ailMel1)), Chain and Net Alignments\
parent chainNetAilMel1\
shortLabel Net\
track chainNetAilMel1Viewnet\
view net\
visibility full\

chainNetCanFam2	Dog Chain/Net	bed 3	Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments	0	410.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of dog (May 2005 (Broad/canFam2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
dog and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
dog assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best dog/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The dog sequence used in this annotation is from\
the May 2005 (Broad/canFam2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the dog/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single dog chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb canFam2\
priority 410.3\
shortLabel Dog Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetCanFam2\
type bed 3\
visibility hide\

chainNetCanFam2Viewchain	Chain	bed 3	Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments	3	410.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments\
parent chainNetCanFam2\
shortLabel Chain\
spectrum on\
track chainNetCanFam2Viewchain\
view chain\
visibility pack\

chainNetCanFam2Viewnet	Net	bed 3	Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments	2	410.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Dog (May 2005 (Broad/canFam2)), Chain and Net Alignments\
parent chainNetCanFam2\
shortLabel Net\
track chainNetCanFam2Viewnet\
view net\
visibility full\

chainNetFelCat4	Cat Chain/Net	bed 3	Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments	0	420.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
cat and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
cat assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best cat/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The cat sequence used in this annotation is from\
the Dec. 2008 (NHGRI/GTB V17e/felCat4) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the cat/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single cat chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb felCat4\
priority 420.3\
shortLabel Cat Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetFelCat4\
type bed 3\
visibility hide\

chainNetFelCat4Viewchain	Chain	bed 3	Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments	3	420.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments\
parent chainNetFelCat4\
shortLabel Chain\
spectrum on\
track chainNetFelCat4Viewchain\
view chain\
visibility pack\

chainNetFelCat4Viewnet	Net	bed 3	Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments	2	420.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Cat (Dec. 2008 (NHGRI/GTB V17e/felCat4)), Chain and Net Alignments\
parent chainNetFelCat4\
shortLabel Net\
track chainNetFelCat4Viewnet\
view net\
visibility full\

chainNetEquCab2	Horse Chain/Net	bed 3	Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments	0	430.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of horse (Sep. 2007 (Broad/equCab2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
horse and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
horse assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best horse/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The horse sequence used in this annotation is from\
the Sep. 2007 (Broad/equCab2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the horse/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single horse chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb equCab2\
priority 430.3\
shortLabel Horse Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetEquCab2\
type bed 3\
visibility hide\

chainNetEquCab2Viewchain	Chain	bed 3	Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments	3	430.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments\
parent chainNetEquCab2\
shortLabel Chain\
spectrum on\
track chainNetEquCab2Viewchain\
view chain\
visibility pack\

chainNetEquCab2Viewnet	Net	bed 3	Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments	2	430.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Horse (Sep. 2007 (Broad/equCab2)), Chain and Net Alignments\
parent chainNetEquCab2\
shortLabel Net\
track chainNetEquCab2Viewnet\
view net\
visibility full\

chainNetOviAri1	Sheep Chain/Net	bed 3	Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments	0	435.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
sheep and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
sheep assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best sheep/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The sheep sequence used in this annotation is from\
the Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the sheep/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single sheep chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb oviAri1\
priority 435.3\
shortLabel Sheep Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetOviAri1\
type bed 3\
visibility hide\

chainNetOviAri1Viewchain	Chain	bed 3	Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments	3	435.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments\
parent chainNetOviAri1\
shortLabel Chain\
spectrum on\
track chainNetOviAri1Viewchain\
view chain\
visibility pack\

chainNetOviAri1Viewnet	Net	bed 3	Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments	2	435.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Sheep (Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1)), Chain and Net Alignments\
parent chainNetOviAri1\
shortLabel Net\
track chainNetOviAri1Viewnet\
view net\
visibility full\

chainNetBosTau6	bosTau6 Chain/Net	bed 3	Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments	0	440.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
cow and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
cow assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best cow/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The cow sequence used in this annotation is from\
the Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the cow/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single cow chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb bosTau6\
priority 440.3\
shortLabel bosTau6 Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetBosTau6\
type bed 3\
visibility hide\

chainNetBosTau6Viewchain	Chain	bed 3	Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments	3	440.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments\
parent chainNetBosTau6\
shortLabel Chain\
spectrum on\
track chainNetBosTau6Viewchain\
view chain\
visibility pack\

chainNetBosTau6Viewnet	Net	bed 3	Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments	2	440.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Cow (Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)), Chain and Net Alignments\
parent chainNetBosTau6\
shortLabel Net\
track chainNetBosTau6Viewnet\
view net\
visibility full\

chainNetSusScr2	Pig Chain/Net	bed 3	Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments	0	465.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
pig and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
pig assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best pig/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The pig sequence used in this annotation is from\
the Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the pig/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single pig chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb susScr2\
priority 465.3\
shortLabel Pig Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetSusScr2\
type bed 3\
visibility hide\

chainNetSusScr2Viewchain	Chain	bed 3	Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments	3	465.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments\
parent chainNetSusScr2\
shortLabel Chain\
spectrum on\
track chainNetSusScr2Viewchain\
view chain\
visibility pack\

chainNetSusScr2Viewnet	Net	bed 3	Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments	2	465.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Pig (Nov. 2009 (SGSC Sscrofa9.2/susScr2)), Chain and Net Alignments\
parent chainNetSusScr2\
shortLabel Net\
track chainNetSusScr2Viewnet\
view net\
visibility full\

chainNetLoxAfr3	Elephant Chain/Net	bed 3	Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments	0	510.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of elephant (Jul. 2009 (Broad/loxAfr3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
elephant and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
elephant assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best elephant/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The elephant sequence used in this annotation is from\
the Jul. 2009 (Broad/loxAfr3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the elephant/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single elephant chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=medium\
\
tableSize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111   72111  152111  252111\
qGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
tGap    350 425 450  600  900  2900  22900  57900  117900  217900  317900\
bothGap 750 825 850 1000 1300  3300  23300  58300  118300  218300  318300\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap medium\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb loxAfr3\
priority 510.3\
shortLabel Elephant Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetLoxAfr3\
type bed 3\
visibility hide\

chainNetLoxAfr3Viewchain	Chain	bed 3	Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments	3	510.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments\
parent chainNetLoxAfr3\
shortLabel Chain\
spectrum on\
track chainNetLoxAfr3Viewchain\
view chain\
visibility pack\

chainNetLoxAfr3Viewnet	Net	bed 3	Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments	2	510.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Elephant (Jul. 2009 (Broad/loxAfr3)), Chain and Net Alignments\
parent chainNetLoxAfr3\
shortLabel Net\
track chainNetLoxAfr3Viewnet\
view net\
visibility full\

chainNetMonDom5	Opossum Chain/Net	bed 3	Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments	0	530.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of opossum (Oct. 2006 (Broad/monDom5)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
opossum and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
opossum assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best opossum/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The opossum sequence used in this annotation is from\
the Oct. 2006 (Broad/monDom5) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the opossum/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single opossum chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;3000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 3000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb monDom5\
priority 530.3\
shortLabel Opossum Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetMonDom5\
type bed 3\
visibility hide\

chainNetMonDom5Viewchain	Chain	bed 3	Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments	3	530.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments\
parent chainNetMonDom5\
shortLabel Chain\
spectrum on\
track chainNetMonDom5Viewchain\
view chain\
visibility pack\

chainNetMonDom5Viewnet	Net	bed 3	Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments	2	530.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Opossum (Oct. 2006 (Broad/monDom5)), Chain and Net Alignments\
parent chainNetMonDom5\
shortLabel Net\
track chainNetMonDom5Viewnet\
view net\
visibility full\

chainNetOrnAna1	Platypus Chain/Net	bed 3	Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments	0	540.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
platypus and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
platypus assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best platypus/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The platypus sequence used in this annotation is from\
the Mar. 2007 (WUGSC 5.0.1/ornAna1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the platypus/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single platypus chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb ornAna1\
priority 540.3\
shortLabel Platypus Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetOrnAna1\
type bed 3\
visibility hide\

chainNetOrnAna1Viewchain	Chain	bed 3	Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments	3	540.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments\
parent chainNetOrnAna1\
shortLabel Chain\
spectrum on\
track chainNetOrnAna1Viewchain\
view chain\
visibility pack\

chainNetOrnAna1Viewnet	Net	bed 3	Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments	2	540.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Platypus (Mar. 2007 (WUGSC 5.0.1/ornAna1)), Chain and Net Alignments\
parent chainNetOrnAna1\
shortLabel Net\
track chainNetOrnAna1Viewnet\
view net\
visibility full\

chainNetAnoCar2	Lizard Chain/Net	bed 3	Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments	0	550.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of lizard (May 2010 (Broad AnoCar2.0/anoCar2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
lizard and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
lizard assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best lizard/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The lizard sequence used in this annotation is from\
the May 2010 (Broad AnoCar2.0/anoCar2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the lizard/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single lizard chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb anoCar2\
priority 550.3\
shortLabel Lizard Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetAnoCar2\
type bed 3\
visibility hide\

chainNetAnoCar2Viewchain	Chain	bed 3	Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments	3	550.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments\
parent chainNetAnoCar2\
shortLabel Chain\
spectrum on\
track chainNetAnoCar2Viewchain\
view chain\
visibility pack\

chainNetAnoCar2Viewnet	Net	bed 3	Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments	2	550.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Lizard (May 2010 (Broad AnoCar2.0/anoCar2)), Chain and Net Alignments\
parent chainNetAnoCar2\
shortLabel Net\
track chainNetAnoCar2Viewnet\
view net\
visibility full\

chainNetMelGal1	Turkey Chain/Net	bed 3	Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments	0	555.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
turkey and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
turkey assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best turkey/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The turkey sequence used in this annotation is from\
the Dec. 2009 (TGC Turkey_2.01/melGal1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the turkey/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single turkey chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments\
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb melGal1\
priority 555.3\
shortLabel Turkey Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetMelGal1\
type bed 3\
visibility hide\

chainNetMelGal1Viewchain	Chain	bed 3	Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments	3	555.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments\
parent chainNetMelGal1\
shortLabel Chain\
spectrum on\
track chainNetMelGal1Viewchain\
view chain\
visibility pack\

chainNetMelGal1Viewnet	Net	bed 3	Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments	2	555.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Turkey (Dec. 2009 (TGC Turkey_2.01/melGal1)), Chain and Net Alignments\
parent chainNetMelGal1\
shortLabel Net\
track chainNetMelGal1Viewnet\
view net\
visibility full\

chainNetGalGal3	Chicken Chain/Net	bed 3	Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments	0	560.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of chicken (May 2006 (WUGSC 2.1/galGal3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
chicken and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
chicken assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best chicken/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The chicken sequence used in this annotation is from\
the May 2006 (WUGSC 2.1/galGal3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the chicken/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single chicken chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb galGal3\
priority 560.3\
shortLabel Chicken Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetGalGal3\
type bed 3\
visibility hide\

chainNetGalGal3Viewchain	Chain	bed 3	Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments	3	560.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments\
parent chainNetGalGal3\
shortLabel Chain\
spectrum on\
track chainNetGalGal3Viewchain\
view chain\
visibility pack\

chainNetGalGal3Viewnet	Net	bed 3	Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments	2	560.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Chicken (May 2006 (WUGSC 2.1/galGal3)), Chain and Net Alignments\
parent chainNetGalGal3\
shortLabel Net\
track chainNetGalGal3Viewnet\
view net\
visibility full\

chainNetXenTro3	X. tropicalis Chain/Net	bed 3	X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments	0	580.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
X. tropicalis and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
X. tropicalis assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best X. tropicalis/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The X. tropicalis sequence used in this annotation is from\
the Nov. 2009 (JGI 4.2/xenTro3) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the X. tropicalis/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single X. tropicalis chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb xenTro3\
priority 580.3\
shortLabel X. tropicalis Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetXenTro3\
type bed 3\
visibility hide\

chainNetXenTro3Viewchain	Chain	bed 3	X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments	3	580.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments\
parent chainNetXenTro3\
shortLabel Chain\
spectrum on\
track chainNetXenTro3Viewchain\
view chain\
visibility pack\

chainNetXenTro3Viewnet	Net	bed 3	X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments	2	580.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel X. tropicalis (Nov. 2009 (JGI 4.2/xenTro3)), Chain and Net Alignments\
parent chainNetXenTro3\
shortLabel Net\
track chainNetXenTro3Viewnet\
view net\
visibility full\

chainNetDanRer7	Zebrafish Chain/Net	bed 3	Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments	0	590.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of zebrafish (Jul. 2010 (Zv9/danRer7)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
zebrafish and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
zebrafish assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best zebrafish/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The zebrafish sequence used in this annotation is from\
the Jul. 2010 (Zv9/danRer7) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the zebrafish/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single zebrafish chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb danRer7\
priority 590.3\
shortLabel Zebrafish Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetDanRer7\
type bed 3\
visibility hide\

chainNetDanRer7Viewchain	Chain	bed 3	Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments	3	590.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments\
parent chainNetDanRer7\
shortLabel Chain\
spectrum on\
track chainNetDanRer7Viewchain\
view chain\
visibility pack\

chainNetDanRer7Viewnet	Net	bed 3	Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments	2	590.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Zebrafish (Jul. 2010 (Zv9/danRer7)), Chain and Net Alignments\
parent chainNetDanRer7\
shortLabel Net\
track chainNetDanRer7Viewnet\
view net\
visibility full\

chainNetGasAcu1	Stickleback Chain/Net	bed 3	Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments	0	600.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of stickleback (Feb. 2006 (Broad/gasAcu1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
stickleback and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
stickleback assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best stickleback/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The stickleback sequence used in this annotation is from\
the Feb. 2006 (Broad/gasAcu1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the stickleback/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single stickleback chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb gasAcu1\
priority 600.3\
shortLabel Stickleback Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetGasAcu1\
type bed 3\
visibility hide\

chainNetGasAcu1Viewchain	Chain	bed 3	Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments	3	600.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments\
parent chainNetGasAcu1\
shortLabel Chain\
spectrum on\
track chainNetGasAcu1Viewchain\
view chain\
visibility pack\

chainNetGasAcu1Viewnet	Net	bed 3	Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments	2	600.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Stickleback (Feb. 2006 (Broad/gasAcu1)), Chain and Net Alignments\
parent chainNetGasAcu1\
shortLabel Net\
track chainNetGasAcu1Viewnet\
view net\
visibility full\

chainNetOryLat2	Medaka Chain/Net	bed 3	Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments	0	610.3	0	0	0	100	50	0	0	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
medaka and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
medaka assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best medaka/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The medaka sequence used in this annotation is from\
the Oct. 2005 (NIG/UT MEDAKA1/oryLat2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the medaka/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single medaka chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb oryLat2\
priority 610.3\
shortLabel Medaka Chain/Net\
sortOrder view=+\
subGroup1 view Views chain=Chain net=Net\
track chainNetOryLat2\
type bed 3\
visibility hide\

chainNetOryLat2Viewchain	Chain	bed 3	Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments	3	610.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments\
parent chainNetOryLat2\
shortLabel Chain\
spectrum on\
track chainNetOryLat2Viewchain\
view chain\
visibility pack\

chainNetOryLat2Viewnet	Net	bed 3	Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments	2	610.3	0	0	0	100	50	0	0	0	0				compGeno	1	longLabel Medaka (Oct. 2005 (NIG/UT MEDAKA1/oryLat2)), Chain and Net Alignments\
parent chainNetOryLat2\
shortLabel Net\
track chainNetOryLat2Viewnet\
view net\
visibility full\

chainNetFr2	Fugu Chain/Net	bed 3	Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments	0	620.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of fugu (Oct. 2004 (JGI 4.0/fr2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
fugu and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
fugu assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best fugu/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The fugu sequence used in this annotation is from\
the Oct. 2004 (JGI 4.0/fr2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the fugu/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single fugu chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb fr2\
priority 620.3\
shortLabel Fugu Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetFr2\
type bed 3\
visibility hide\

chainNetFr2Viewchain	Chain	bed 3	Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments	3	620.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments\
parent chainNetFr2\
shortLabel Chain\
spectrum on\
track chainNetFr2Viewchain\
view chain\
visibility pack\

chainNetFr2Viewnet	Net	bed 3	Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments	2	620.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Fugu (Oct. 2004 (JGI 4.0/fr2)), Chain and Net Alignments\
parent chainNetFr2\
shortLabel Net\
track chainNetFr2Viewnet\
view net\
visibility full\

chainNetTetNig2	Tetraodon Chain/Net	bed 3	Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments	0	630.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
tetraodon and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
tetraodon assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best tetraodon/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The tetraodon sequence used in this annotation is from\
the Mar. 2007 (Genoscope 8.0/tetNig2) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the tetraodon/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single tetraodon chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb tetNig2\
priority 630.3\
shortLabel Tetraodon Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetTetNig2\
type bed 3\
visibility hide\

chainNetTetNig2Viewchain	Chain	bed 3	Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments	3	630.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments\
parent chainNetTetNig2\
shortLabel Chain\
spectrum on\
track chainNetTetNig2Viewchain\
view chain\
visibility pack\

chainNetTetNig2Viewnet	Net	bed 3	Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments	2	630.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Tetraodon (Mar. 2007 (Genoscope 8.0/tetNig2)), Chain and Net Alignments\
parent chainNetTetNig2\
shortLabel Net\
track chainNetTetNig2Viewnet\
view net\
visibility full\

chainNetPetMar1	Lamprey Chain/Net	bed 3	Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments	0	640.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of lamprey (Mar. 2007 (WUGSC 3.0/petMar1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
lamprey and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
lamprey assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best lamprey/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The lamprey sequence used in this annotation is from\
the Mar. 2007 (WUGSC 3.0/petMar1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the lamprey/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single lamprey chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
chainLinearGap loose\
chainMinScore 5000\
color 0,0,0\
compositeTrack on\
dragAndDrop subTracks\
group compGeno\
html chainNet\
longLabel Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments\
matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\
matrixHeader A, C, G, T\
noInherit on\
otherDb petMar1\
priority 640.3\
shortLabel Lamprey Chain/Net\
sortOrder view=+\
spectrum on\
subGroup1 view Views chain=Chain net=Net\
track chainNetPetMar1\
type bed 3\
visibility hide\

chainNetPetMar1Viewchain	Chain	bed 3	Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments	3	640.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments\
parent chainNetPetMar1\
shortLabel Chain\
spectrum on\
track chainNetPetMar1Viewchain\
view chain\
visibility pack\

chainNetPetMar1Viewnet	Net	bed 3	Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments	2	640.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Lamprey (Mar. 2007 (WUGSC 3.0/petMar1)), Chain and Net Alignments\
parent chainNetPetMar1\
shortLabel Net\
track chainNetPetMar1Viewnet\
view net\
visibility full\

chainNetBraFlo1	Lancelet Chain/Net	bed 3	Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments	0	660.3	0	0	0	100	50	0	1	0	0			<H2>Description</H2>\
<P>\
This track shows regions of the genome that are alignable\
to other genomes (&quot;chain&quot; subtracks) or in synteny (&quot;net&quot; subtracks).\
The alignable parts are shown with thick blocks that look like exons. \
Non-alignable parts between these are shown like introns.\
</P>\
\
<H3>Chain Track</H3>\
<P>\
The chain track shows alignments of lancelet (Mar. 2006 (JGI 1.0/braFlo1)) to the\
mouse genome using a gap scoring system that allows longer gaps \
than traditional affine gap scoring systems. It can also tolerate gaps in both\
lancelet and mouse simultaneously. These \
&quot;double-sided&quot; gaps can be caused by local inversions and \
overlapping deletions in both species. \
<P>\
The chain track displays boxes joined together by either single or\
double lines. The boxes represent aligning regions.\
Single lines indicate gaps that are largely due to a deletion in the\
lancelet assembly or an insertion in the mouse \
assembly.  Double lines represent more complex gaps that involve substantial\
sequence in both species. This may result from inversions, overlapping\
deletions, an abundance of local mutation, or an unsequenced gap in one\
species.  In cases where multiple chains align over a particular region of\
the mouse genome, the chains with single-lined gaps are often \
due to processed pseudogenes, while chains with double-lined gaps are more \
often due to paralogs and unprocessed pseudogenes.</P> \
<P>\
In the &quot;pack&quot; and &quot;full&quot; display\
modes, the individual feature names indicate the chromosome, strand, and\
location (in thousands) of the match for each matching alignment.</P>\
\
<H3>Net Track</H3>\
<P>\
The net track shows the best lancelet/mouse chain for \
every part of the mouse genome. It is useful for\
finding syntenic regions, possibly orthologs, and for studying genome\
rearrangement.  The lancelet sequence used in this annotation is from\
the Mar. 2006 (JGI 1.0/braFlo1) assembly.</P>\
\
<H2>Display Conventions and Configuration</H2>\
<H3>Chain Track</H3>\
<P>By default, the chains to chromosome-based assemblies are colored\
based on which chromosome they map to in the aligning organism. To turn\
off the coloring, check the &quot;off&quot; button next to: Color\
track based on chromosome.</P>\
<P>\
To display only the chains of one chromosome in the aligning\
organism, enter the name of that chromosome (e.g. chr4) in box next to: \
Filter by chromosome.</P>\
\
<H3>Net Track</H3>\
<P>\
In full display mode, the top-level (level 1)\
chains are the largest, highest-scoring chains that\
span this region.  In many cases gaps exist in the\
top-level chain.  When possible, these are filled in by\
other chains that are displayed at level 2.  The gaps in \
level 2 chains may be filled by level 3 chains and so\
forth. </P>\
<P>\
In the graphical display, the boxes represent ungapped \
alignments; the lines represent gaps.  Click\
on a box to view detailed information about the chain\
as a whole; click on a line to display information\
about the gap.  The detailed information is useful in determining\
the cause of the gap or, for lower level chains, the genomic\
rearrangement. </P> \
<P> \
Individual items in the display are categorized as one of four types\
(other than gap):</P>\
<P><UL>\
<LI><B>Top</B> - the best, longest match. Displayed on level 1.\
<LI><B>Syn</B> - line-ups on the same chromosome as the gap in the level above\
it.\
<LI><B>Inv</B> - a line-up on the same chromosome as the gap above it, but in \
the opposite orientation.\
<LI><B>NonSyn</B> - a match to a chromosome different from the gap in the \
level above.\
</UL></P>\
\
<H2>Methods</H2>\
<H3>Chain track</H3>\
<P>\
Transposons that have been inserted since the lancelet/mouse\
split were removed from the assemblies. The abbreviated genomes were\
aligned with lastz, and the transposons were added back in.\
The resulting alignments were converted into axt format using the lavToAxt\
program. The axt alignments were fed into axtChain, which organizes all\
alignments between a single lancelet chromosome and a single\
mouse chromosome into a group and creates a kd-tree out\
of the gapless subsections (blocks) of the alignments. A dynamic program\
was then run over the kd-trees to find the maximally scoring chains of these\
blocks.\
\
The following matrix was used:<P>\
<BLOCKQUOTE><TABLE class='chainTbl'>\
<TR ALIGN=right><TD>&nbsp;</TD><TD><B>A</B></TD><TD><B>C</B></TD><TD><B>G</B></TD><TD><B>T</B></TD></TR>\
<TR ALIGN=right><TD><B>A<B></TD><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>\
<TR ALIGN=right><TD><B>C<B></TD><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>\
<TR ALIGN=right><TD><B>G<B></TD><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>\
<TR ALIGN=right><TD><B>T<B></TD><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>\
</TABLE></BLOCKQUOTE></P>\
\
\
Chains scoring below a minimum score of &quot;5000&quot; were discarded;\
the remaining chains are displayed in this track.  The linear gap\
matrix used with axtChain:<BR>\
<PRE>-linearGap=loose\
\
tablesize    11\
smallSize   111\
position  1   2   3   11  111  2111  12111  32111  72111  152111  252111\
qGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
tGap    325 360 400  450  600  1100   3600   7600  15600   31600   56600\
bothGap 625 660 700  750  900  1400   4000   8000  16000   32000   57000\
</PRE>\
</P>\
\
<H3>Net track</H3>\
<P>\
Chains were derived from lastz alignments, using the methods\
described on the chain tracks description pages, and sorted with the \
highest-scoring chains in the genome ranked first. The program\
chainNet was then used to place the chains one at a time, trimming them as \
necessary to fit into sections not already covered by a higher-scoring chain. \
During this process, a natural hierarchy emerged in which a chain that filled \
a gap in a higher-scoring chain was placed underneath that chain. The program \
netSyntenic was used to fill in information about the relationship between \
higher- and lower-level chains, such as whether a lower-level\
chain was syntenic or inverted relative to the higher-level chain. \
The program netClass was then used to fill in how much of the gaps and chains \
contained <em>N</em>s (sequencing gaps) in one or both species and how much\
was filled with transposons inserted before and after the two organisms \
diverged.</P>\
\
<H2>Credits</H2>\
<P>\
Lastz (previously known as blastz) was developed at\
<A HREF="http://www.bx.psu.edu/miller_lab/" \
TARGET=_blank>Pennsylvania State University</A> by \
Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\
Ross Hardison.</P>\
<P>\
Lineage-specific repeats were identified by Arian Smit and his \
<A HREF="http://www.repeatmasker.org" TARGET=_blank>RepeatMasker</A>\
program.</P>\
<P>\
The axtChain program was developed at the University of California at \
Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.</P>\
<P>\
The browser display and database storage of the chains and nets were created\
by Robert Baertsch and Jim Kent.</P>\
<P>\
The chainNet, netSyntenic, and netClass programs were\
developed at the University of California\
Santa Cruz by Jim Kent.</P>\
<P>\
\
<h2>References</h2>\
\
<p>\
Harris, R.S.\
<a href="http://www.bx.psu.edu/~rsharris/lastz/"\
target=_blank>(2007) Improved pairwise alignment of genomic DNA</a>\
Ph.D. Thesis, The Pennsylvania State University\
</p>\
\
<p>\
Chiaromonte F, Yap VB, Miller W.\
<A HREF="http://psb.stanford.edu/psb-online/proceedings/psb02/chiaromonte.pdf"\
TARGET=_blank>Scoring pairwise genomic sequence alignments</A>.\
<em>Pac Symp Biocomput</em>. 2002:115-26.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11928468" target="_blank">11928468</a>\
</p>\
\
<P>\
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\
<A HREF="https://www.pnas.org/content/100/20/11484"\
TARGET=_blank>Evolution's cauldron:\
duplication, deletion, and rearrangement in the mouse and human genomes</A>.\
<em>Proc Natl Acad Sci U S A</em>. 2003 Sep 30;100(20):11484-9.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/14500911" target="_blank">14500911</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208784/" target="_blank">PMC208784</a>\
</p>\
\
<P>\
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\
Haussler D, Miller W.\
<A HREF="https://genome.cshlp.org/content/13/1/103.abstract"\
TARGET=_blank>Human-mouse alignments with BLASTZ</A>.\
<em>Genome Res</em>. 2003 Jan;13(1):103-7.\
PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/12529312" target="_blank">12529312</a>; PMC: <a\
href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430961/" target="_blank">PMC430961</a>\
</p>\
	compGeno	1	altColor 100,50,0\
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html chainNet\
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matrixHeader A, C, G, T\
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chainNetBraFlo1Viewchain	Chain	bed 3	Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments	3	660.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments\
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chainNetBraFlo1Viewnet	Net	bed 3	Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments	2	660.3	0	0	0	100	50	0	1	0	0				compGeno	1	longLabel Lancelet (Mar. 2006 (JGI 1.0/braFlo1)), Chain and Net Alignments\
parent chainNetBraFlo1\
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