## Description

This track is produced as part of the mouse ENCODE Project. This track shows RNA-seq measured genome-wide in mouse tissues and cell lines using the RNA-seq methodology (see below), and DNaseI hypersensitive sites.

## Display Conventions and Configuration

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

Plus and Minus Signals
  These views display clusters of overlapping read mappings on the forward and reverse genomic strands
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. Fresh tissues were harvested from mice and the nuclei prepared according to the tissue appropriate protocol.

Reads were aligned to mm9 reference using ABI BioScope software version 1.2.1. Colorspace FASTQ format files were created using Heng Li's solid2fastq.pl script version 0.1.4, representing 0,1,2,3 color codes with the letters A,C,G,T respectively. Signal files were created from the BAM alignments using BEDTools.

## Verification

## Credits

These data were generated by the UW ENCODE group.

Contact: Richard Sandstrom

## References

## 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Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset.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, above. The full data release policy for ENCODE is available here.