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RNA-seq from ENCODE/LICR   (All Expression and Regulation tracks)

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 Cerebellum  Signal  Adult 8 weeks  1  Cerebellum Adult 8 weeks RNA-seq Signal Rep 1 from ENCODE/LICR    Schema   2012-02-11 
 
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 Whole Brain  Signal  Embryonic day 14.5  1  Whole Brain Embryonic day 14.5 RNA-seq Signal Rep 1 from ENCODE/LICR    Schema   2012-10-03 
 
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Description

Using RNA-seq (Mortazavi et al., 2008), high-resolution genome-wide maps of the mouse transcriptome in various mouse (C57BL/6) tissues, primary cells, cell lines of different developmental stage and age groups were generated.

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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. See the SAM Format Specification for more information on the SAM/BAM file format.

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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). Long 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 NCBI37/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).

Release Notes

This is Release 2 (Mar 2012). It contains a total of 22 RNA-seq experiments with the addition of 12 new experiments.

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 BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. PMID: 18516045

Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Oct;37(18):e123. PMID: 19620212; PMC: PMC2764448

Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. PMID: 19289445; PMC: PMC2672628

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. PMID: 20436464; PMC: PMC3146043

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.