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Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs

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Show simple item record Guttman, Mitchell Garber, Manuel Levin, Joshua Z. Donaghey, Julie Robinson, James Adiconis, Xian Fan, Lin Koziol, Magdalena J. Gnirke, Andreas Nusbaum, Chad Rinn, John L. Lander, Eric S. Regev, Aviv 2012-10-12T18:54:20Z 2012-10-12T18:54:20Z 2010-07 2010-03
dc.identifier.issn 1087-0156
dc.identifier.issn 1546-1696
dc.description available in PMC 2010 November 2. en_US
dc.description.abstract RNA-Seq provides an unbiased way to study a transcriptome, including both coding and noncoding genes. To date, most RNA-Seq studies have critically depended on existing annotations, and thus focused on expression levels and variation in known transcripts. Here, we present Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence. We apply it to mouse embryonic stem cells, neuronal precursor cells, and lung fibroblasts to accurately reconstruct the full-length gene structures for the vast majority of known expressed genes. We identify substantial variation in protein-coding genes, including thousands of novel 5′-start sites, 3′-ends, and internal coding exons. We then determine the gene structures of over a thousand lincRNA and antisense loci. Our results open the way to direct experimental manipulation of thousands of non-coding RNAs, and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes. en_US
dc.description.sponsorship Merkin Family Foundation for Stem Cell Research en_US
dc.description.sponsorship Howard Hughes Medical Institute en_US
dc.description.sponsorship National Human Genome Research Institute (U.S.) en_US
dc.description.sponsorship Burroughs Wellcome Fund en_US
dc.description.sponsorship Broad Institute en_US
dc.language.iso en_US
dc.publisher Nature Publishing Group en_US
dc.relation.isversionof en_US
dc.rights Creative Commons Attribution-Noncommercial-Share Alike 3.0 en_US
dc.rights.uri en_US
dc.source PMC en_US
dc.title Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs en_US
dc.title.alternative Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs en_US
dc.type Article en_US
dc.identifier.citation Guttman, Mitchell et al. “Ab Initio Reconstruction of Cell Type–specific Transcriptomes in Mouse Reveals the Conserved Multi-exonic Structure of lincRNAs.” Nature Biotechnology 28.5 (2010): 503–510. Web. en_US
dc.contributor.department Massachusetts Institute of Technology. Department of Biology en_US
dc.contributor.mitauthor Guttman, Mitchell
dc.contributor.mitauthor Lander, Eric S.
dc.contributor.mitauthor Regev, Aviv
dc.relation.journal Nature Biotechnology en_US
dc.identifier.mitlicense OPEN_ACCESS_POLICY en_US
dc.eprint.version Author's final manuscript en_US
dc.type.uri en_US
eprint.status en_US
dspace.orderedauthors Guttman, Mitchell; Garber, Manuel; Levin, Joshua Z; Donaghey, Julie; Robinson, James; Adiconis, Xian; Fan, Lin; Koziol, Magdalena J; Gnirke, Andreas; Nusbaum, Chad; Rinn, John L; Lander, Eric S; Regev, Aviv en

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