Description

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 either GENCODE M4 or M21 annotations.

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 four sub tracks are:

• timecourse M4 TPM – TPM values using GENCODE M4 annotations
• timecourse M4 FPKM – FPKM values using GENCODE M4 annotations
• timecourse M21 TPM – TPM values using GENCODE M21 annotations
• timecourse M21 FPKM – FPKM values using GENCODE M21 annotations

Display Conventions and Configuration

Each sub track is displayed as a bigBarChart. Bar charts show expression levels for each sample, colored by tissue type. The tracks can be faceted by tissue and timepoint using the track configuration controls.

Bars are colored by tissue:

Within each tissue, bars are grouped by developmental time point: e10.5, e11.5, e12.5, e13.5, e14.5, e15.5, e16.5, and P0. Not all tissues are available at all time points.

Methods

RNA-seq reads were processed using the ENCODE long RNA-seq pipeline. Reads were aligned to the mm10 genome using STAR and quantified at the gene level using RSEM. For each annotation set (GENCODE M4 and M21), 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), and the bed file was converted into a bigBarChart bigBed file.

Data Access

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.

Credits

Peng He (Peng.He@ucsf.edu) was the lead author for this project and performed the data analysis. Diane Trout (diane@caltech.edu) at the Wold Lab, Caltech, was responsible for data management. The data were produced as part of the ENCODE Consortium.

References

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. PMID: 23104886; PMC: PMC3530905

Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011 Aug 4;12:323. PMID: 21816040; PMC: PMC3163565