NDLI: Mapping and quantifying mammalian transcriptomes by RNA-Seq.

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Mapping and quantifying mammalian transcriptomes by RNA-Seq.

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Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Mortazavi, Ali Williams, Brian A. McCue, Kenneth Schaeffer, Lorian Wold, Barbara
Description	Country affiliation: United States Author Affiliation: Mortazavi A ( Division of Biology, MC 156-29, California Institute of Technology, Pasadena, California 91125, USA.)
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 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.
File Format	HTM / HTML
ISSN	15487091
Issue Number	7
Volume Number	5
e-ISSN	15487105
Journal	Nature Methods
Language	English
Publisher	Nature Publishing Group
Publisher Date	2008-07-01
Publisher Place	United States
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Discipline Clinical Laboratory Techniques Gene Expression Profiling Methods Rna Genetics Sequence Analysis, Rna 3' Untranslated Regions Algorithms Alternative Splicing Animals Brain Metabolism Chromosome Mapping Databases, Nucleic Acid Exons Statistics & Numerical Data Liver Mice Mice, Inbred C57bl Muscle, Skeletal Oligonucleotide Array Sequence Analysis Promoter Regions, Genetic Rna Splicing Rna, Messenger Sensitivity And Specificity Software Journal Article Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Cell Biology Biochemistry Molecular Biology Biotechnology

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