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 shown as its own bar. Bars can be filtered by tissue and time point using the track configuration controls.
The two subtracks 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 mm39 annotations were lifted from mm10. Of the 55,536 genes in the mm10 GENCODE M21 data, 55,447 lifted successfully and 89 did not. Of those 89, 42 are on chr14 and 40 of those fall within chr14:3.2-26.3 Mb; about half carry Gm or Rik names, indicating predicted rather than curated genes. The gene Il11ra2 appears three times. Two of those copies sit at the same position, chr4:42,656,355-42,661,893, because a copy that is on an unplaced scaffold in mm10 lifted onto the same place as the copy on the main chromosome. Both carry the same expression values, and clicking either one opens the same details page. The third copy is about 497 kb away, at chr4:42,159,195-42,164,733.
The steps and scripts used to build this track are documented in our makedoc, and the track configuration is in mouseDevTimecourse.ra.
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.