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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Cells were grown according to the approved ENCODE cell culture protocols.
This is Release 2 (Mar 2012). It contains a total of 22 RNA-seq experiments with the addition of 12 new experiments.
These data were generated and analyzed in Bing Ren's laboratory at the Ludwig Institute for Cancer Research.
Contact: Yin Shen
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.
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.
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11.
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.
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