Mapping and quantifying mammalian transcriptomes by RNA-Seq Export

@article{citeulike:2860398, abstract = {We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41–52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although >90\% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 105 distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.}, address = {[1] Division of Biology, MC 156-29, California Institute of Technology, Pasadena, California 91125, USA. [2] These authors contributed equally to this work.}, author = {Mortazavi, Ali and Williams, Brian A. and McCue, Kenneth and Schaeffer, Lorian and Wold, Barbara}, booktitle = {Nat Meth}, citeulike-article-id = {2860398}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nmeth.1226}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nmeth.1226}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18516045}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18516045}, day = {30}, doi = {10.1038/nmeth.1226}, issn = {1548-7105}, journal = {Nature Methods}, keywords = {expression, solexa, wga}, month = {May}, number = {7}, pages = {621--628}, posted-at = {2008-07-31 19:20:17}, priority = {2}, publisher = {Nature Publishing Group}, title = {Mapping and quantifying mammalian transcriptomes by RNA-Seq}, url = {http://dx.doi.org/10.1038/nmeth.1226}, volume = {5}, year = {2008} }

TY - JOUR ID - citeulike:2860398 L3 - citeulike-article-id:2860398 N2 - We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41–52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 105 distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices. IS - 7 JF - Nature Methods SN - 1548-7105 AD - [1] Division of Biology, MC 156-29, California Institute of Technology, Pasadena, California 91125, USA. [2] These authors contributed equally to this work. EP - 628 TI - Mapping and quantifying mammalian transcriptomes by RNA-Seq PB - Nature Publishing Group VL - 5 T2 - Nat Meth SP - 621 KW - expression KW - solexa KW - wga AU - Mortazavi, Ali AU - Williams, Brian AU - McCue, Kenneth AU - Schaeffer, Lorian AU - Wold, Barbara PY - 2008/05/30/ UR - http://dx.doi.org/10.1038/nmeth.1226 ER -