This track set displays bulk RNA-seq gene expression data from a mouse developmental time course, covering 17 tissues across up to 8 time points (embryonic days 10.5 through 16.5 and postnatal day 0). Expression values (FPKM and TPM) were generated by RSEM from alignments to the mm10 reference genome using GENCODE M21 annotations and lifted over to the mm39 reference genome.
The data were produced as part of the ENCODE project at the Wold Lab, Caltech. Each tissue and time point has two biological replicates, each displayed as its own bar.
The two sub tracks are:
RNA-seq reads were processed using the ENCODE long RNA-seq pipeline. Reads were aligned to the mm10 genome using STAR (Dobin et al., 2013) and quantified at the gene level using RSEM (Li and Dewey, 2011) with the GENCODE M21 annotation set. The FPKM or TPM column from the RSEM gene quantification files across all tissues and replicates was concatenated into a single matrix. This matrix was then converted into the UCSC faceted bigBarChart format (bed, categories, and facet files). The bed file was converted to the mm39 genome using liftOver and then converted into a bigBarChart bigBed file.
The data in this track can be explored interactively with the Table Browser or the Data Integrator. For programmatic access, the track can be accessed using the Genome Browser's REST API.
The bigBarChart bigBed files underlying this track can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, 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 here.
The original data files and experimental metadata are available from the ENCODE Portal.
Please refer to our Data Access FAQ for more information.