## Description

Using RNA-Seq (Mortazavi et al., 2008), high-resolution genome-wide maps of the mouse transcriptome across multiple mouse (C57Bl/6) tissues and primary cells were generated.

## Display Conventions and Configuration

This is a composite track that contains multiple data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring composite tracks are here. This track contains the following views:

Signal
  Density graph (wiggle) of signal enrichment based on processed data.
Alignments
  Mappings of short reads to the genome.

## Methods

Cells were grown according to the approved ENCODE cell culture protocols.

RNA-Seq
RNA samples from tissues and primary cells were extracted from Trizol® according to protocol (Invitrogen). PolyA+ RNA was purified with the Dynabeads mRNA purification kit (Invitrogen). The mRNA libraries were prepared for strand-specific sequencing as described previously (Parkhomchuk et al., 2009).

Sequencing and Analysis
Samples were sequenced on Illumina Genome Analyzer II, Genome Analyzer IIx and HiSeq 2000 platforms for 36 cycles. Image analysis, base calling and alignment to the mouse genome version mm9 were performed using Illumina's RTA. Alignment to the mouse genome was performed using TopHat (Trapnell et al., 2009). Wig files were generated by TopHat and expression levels were calculated with Cufflinks (Trapnell et al., 2010).

## Credits

These data were generated and analyzed in Bing Ren's laboratory at the Ludwig Institute for Cancer Research.

Contact: Yin Shen

## References

Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008 May; 5: 621-628.

Parkhomchuk, D., Borodina, T., Amstislavskiy, V., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H., and Soldatov, A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 2009 Jun; 37(18): e123.

Trapnell C, Pachter L, and Salzberg SL TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009 Feb; 25(9): 1105-1111.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, and Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature 2010 Feb; 28: 511-515.

## Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column on the track configuration page and the download page. The full data release policy for ENCODE is available here.