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 Configure 		 Cerebrum  Minus Raw Signal  1  adult-8wks  C57BL/6  M  Cerebrum Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW    Data format   2012-03-28 
 
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 Configure 		 Cerebrum  Plus Raw Signal  2  adult-8wks  C57BL/6  M  Cerebrum Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW    Data format   2012-03-28 
 
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 Configure 		 Cerebrum  Signal  1  adult-8wks  C57BL/6  M  Cerebrum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW    Data format   2012-03-28 
 
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 Configure 		 Cerebrum  Signal  2  adult-8wks  C57BL/6  M  Cerebrum Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW    Data format   2012-03-28 
 
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 Configure 		 Heart  Minus Raw Signal  1  adult-8wks  C57BL/6  M  Heart Adult 8 weeks RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW    Data format   2012-09-22 
 
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 Configure 		 Heart  Minus Raw Signal  2  adult-8wks  C57BL/6  M  Heart Adult 8 weeks RNA-seq Minus Raw Signal Rep 2 from ENCODE/UW    Data format   2012-09-22 
 
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 Configure 		 Heart  Plus Raw Signal  1  adult-8wks  C57BL/6  M  Heart Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW    Data format   2012-09-22 
 
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 Configure 		 Heart  Plus Raw Signal  2  adult-8wks  C57BL/6  M  Heart Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW    Data format   2012-09-22 
 
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 Configure 		 Heart  Signal  1  adult-8wks  C57BL/6  M  Heart Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW    Data format   2012-09-22 
 
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 Configure 		 Heart  Signal  2  adult-8wks  C57BL/6  M  Heart Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW    Data format   2012-09-22 
 
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 Configure 		 Liver  Minus Raw Signal  1  E14.5  129  M  Liver 129 Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW    Data format   2012-11-12 
 
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 Configure 		 Liver  Plus Raw Signal  1  E14.5  129  M  Liver 129 Embryonic day 14.5 RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW    Data format   2012-11-12 
 
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 Configure 		 Liver  Plus Raw Signal  1  adult-8wks  C57BL/6  M  Liver C57BL6 Adult 8 weeks RNA-seq Plus Raw Signal Rep 1 from ENCODE/UW    Data format   2012-03-28 
 
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 Configure 		 Liver  Plus Raw Signal  2  adult-8wks  C57BL/6  M  Liver C57BL6 Adult 8 weeks RNA-seq Plus Raw Signal Rep 2 from ENCODE/UW    Data format   2012-03-28 
 
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 Configure 		 Liver  Signal  1  adult-8wks  C57BL/6  M  Liver C57BL6 Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/UW    Data format   2012-03-28 
 
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 Configure 		 Liver  Signal  2  adult-8wks  C57BL/6  M  Liver C57BL6 Adult 8 weeks RNA-seq Signal Rep 2 from ENCODE/UW    Data format   2012-03-28 
 
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 Configure 		 Liver  Minus Raw Signal  1  E14.5  C57BL/6  M  Liver C57BL6 Embryonic day 14.5 RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW    Data format   2012-03-28 
 
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 Configure 		 MEL  Minus Raw Signal  1  immortalized  Unknown  M  MEL Immortal Cells RNA-seq Minus Raw Signal Rep 1 from ENCODE/UW    Data format   2012-03-28 
 
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     Restriction Policy
Assembly: Mouse July 2007 (NCBI37/mm9)

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.