Description

This track displays RNA-seq signal (read coverage) from the same mouse developmental time course bulk RNA-seq experiment shown in the ENCODE Expression bigBarChart tracks, covering 17 tissues across up to 8 time points (embryonic days 10.5 through 16.5 and postnatal day 0). While the bigBarChart tracks show gene-level TPM and FPKM summary values, this track shows the underlying per-base signal that those values were derived from.

For each of the 156 samples (78 tissue/time point combinations, each with two biological replicates), two signal tracks are provided: one from reads that align uniquely to the genome (Unique reads), and one that includes all aligned reads, including reads that map to multiple locations (All reads).

The data were produced as part of the ENCODE project at the Wold Lab, Caltech.

Display Conventions and Configuration

Tracks are organized into two views, Unique reads and All reads. Within each view, subtracks are arranged in a matrix by developmental time point and tissue, with a Replicate filter (Rep 1, Rep 2). By default, only the Unique reads view and Rep 1 are visible; use the track configuration matrix to turn on other tissues, time points, replicates, or the All reads view.

Tracks are colored by tissue, with a gradient that darkens as the time point advances through the eight developmental time points (e10.5, e11.5, e12.5, e13.5, e14.5, e15.5, e16.5, and P0), matching the colors used in the ENCODE Expression bigBarChart tracks. Not all tissues are available at all time points.

Methods

RNA-seq reads were processed using the ENCODE Bulk RNA-seq pipeline. Reads were aligned to the mm10 genome using STAR (Dobin et al., 2013), which reports signal separately for reads that align uniquely to the genome and for all aligned reads, including reads that map to multiple locations. These bigWig signal files were obtained from the ENCODE Portal for each sample and replicate.

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 bigWig files underlying this track can be downloaded from our download server. Individual regions or the whole genome annotation can be obtained using our tool bigWigToWig, 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.