Description
This track was produced as part of the mouse ENCODE Project.
This track shows RNA-seq measured genome-wide in mouse
tissues and cell lines.
Poly-A selected mRNA was used as the source for transcriptome profiling of tissues and cell types
that also had corresponding DNase I hypersensitive profiles.
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.
Color differences among the views are arbitrary and they provide a visual cue for distinguishing
between the different cell and tissue types. 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 50-base single end reads to the genome. See the SAM Format Specification for more information on the SAM/BAM file format.
-
Methods
Cells were grown according to the approved
ENCODE cell culture protocols.
Fresh tissues were harvested from mice and stored until used for preparing total RNA samples. The total RNA
was used as starting material to select poly-A RNA and used for constructing SOLiD libraries according to the
protocols supplied by the manufacturer. All RNA samples were spiked in with NIST standards before libraries were constructed.
The RNA-seq libraries were sequenced on ABI SOLiD sequencing platform as 50-base reads according to the manufacturer's recommendations.
Reads were aligned to the mm9 reference genome 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 (Li et al., 2009a), representing 0, 1, 2, 3 color codes with the letters A, C, G, T respectively.
Signal files were created from the BAM (Li et al., 2009b) alignments using BEDTools (Quinlan et al., 2010).
Release Notes
This is Release 1 (July 2012). It contains a total of 25 RNA-seq experiments.
Credits
These data were generated by the UW ENCODE group.
Contact:
Richard Sandstrom
References
Li H, Durbin R.
Fast and accurate short read alignment with Burrows-Wheeler transform.
Bioinformatics. 2009 Jul 15;25(14):1754-60.
PMID: 19451168; PMC: PMC2705234
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome
Project Data Processing Subgroup.
The Sequence Alignment/Map format and SAMtools.
Bioinformatics. 2009 Aug 15;25(16):2078-9.
PMID: 19505943; PMC: PMC2723002
Quinlan AR, Hall IM.
BEDTools: a flexible suite of utilities for comparing genomic features.
Bioinformatics. 2010 Mar 15;26(6):841-2.
PMID: 20110278; PMC: PMC2832824
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.
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