Description

RNA-seq
This super track groups RNA-seq data from mouse hematopoietic cell types as part of the VISION project (ValIdated Systematic IntegratiON of hematopoietic epigenomes). The tracks provide a genome-wide view of transcriptional activity across blood cell types and cell lines, complementing the epigenomic data used for chromatin state analysis in the VISION project.

This super track contains the following composite tracks:

PolyA+ RNA-seq

RNA-seq signal from the polyA+ fraction of RNA isolated from several hematopoietic cell types in adult mice plus the cell line system G1E and G1E-ER4, including directional and non-directional data.

Differential Expression

Differential expression of genes computed with EBSeq-HMM along branches of myeloid hematopoietic differentiation in mouse, visualized as bar plots of expression levels.

RNA Lara-Astiaso

RNA-seq signal from single-read, unstranded libraries in hematopoietic cell types from Lara-Astiaso et al. (2014).

Display Conventions and Configuration

The track names give an abbreviation for the blood cell type or cell line. Biological replicates are distinguished by a VISION sample id at the beginning of the track name.

Mouse primary blood cells purified predominantly using cell surface markers include: LSK = Lin-Sca1+Kit+ cells from mouse bone marrow containing hematopoietic stem and progenitor cells, CMP = common myeloid progenitor cell, MEP = megakaryocyte-erythrocyte progenitor cell, ERY = erythroblast, GMP = granulocyte monocyte progenitor cell, MON = monocyte, NEU = neutrophil, CFUE = colony forming unit erythroid, CFUMK = colony forming unit megakaryocyte, iMK = immature megakaryocyte, MK_fl = megakaryocyte derived from fetal liver. AVE is a track with state assignments based on the average signal for each epigenetic feature across cell types.

Credits

Belinda Giardine generated the tracks displayed and developed the track hub.

References

Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E, Keren-Shaul H, Mildner A, Winter D, Jung S, Friedman N, Amit I. Immunogenetics. Chromatin state dynamics during blood formation. Science. 2014 Aug 22;345(6199):943-9. doi: 10.1126/science.1256271. PMID: 25103404; PMCID: PMC4412442.

Leng N, Li Y, McIntosh BE, Nguyen BK, Duffin B, Tian S, Thomson JA, Dewey CN, Stewart R, Kendziorski C. EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. Bioinformatics. 2015 Aug 15;31(16):2614-22. doi: 10.1093/bioinformatics/btv193. PMID: 25847007; PMCID: PMC4528625.

Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Res. 2024 Aug 20;34(7):1089-1105. PMID: 38951027; PMCID: PMC11368181.

Data Release Policy

These data are available for use without restrictions.

Contact

Ross Hardison rch8@psu.edu