Mapping and quantifying mammalian transcriptomes by RNA-Seq
- PMID: 18516045
- DOI: 10.1038/nmeth.1226
Mapping and quantifying mammalian transcriptomes by RNA-Seq
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.
Comment in
-
The beginning of the end for microarrays?Nat Methods. 2008 Jul;5(7):585-7. doi: 10.1038/nmeth0708-585. Nat Methods. 2008. PMID: 18587314 No abstract available.
Similar articles
-
ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.Bioinformatics. 2014 Mar 1;30(5):644-51. doi: 10.1093/bioinformatics/btt591. Epub 2013 Oct 15. Bioinformatics. 2014. PMID: 24130305
-
JAGuaR: junction alignments to genome for RNA-seq reads.PLoS One. 2014 Jul 25;9(7):e102398. doi: 10.1371/journal.pone.0102398. eCollection 2014. PLoS One. 2014. PMID: 25062255 Free PMC article.
-
Prediction and Quantification of Splice Events from RNA-Seq Data.PLoS One. 2016 May 24;11(5):e0156132. doi: 10.1371/journal.pone.0156132. eCollection 2016. PLoS One. 2016. PMID: 27218464 Free PMC article.
-
Mapping RNA-seq Reads with STAR.Curr Protoc Bioinformatics. 2015 Sep 3;51:11.14.1-11.14.19. doi: 10.1002/0471250953.bi1114s51. Curr Protoc Bioinformatics. 2015. PMID: 26334920 Free PMC article. Review.
-
RNA-Seq: a revolutionary tool for transcriptomics.Nat Rev Genet. 2009 Jan;10(1):57-63. doi: 10.1038/nrg2484. Nat Rev Genet. 2009. PMID: 19015660 Free PMC article. Review.
Cited by
-
Comparative transcriptome analysis of cucumber fruit tissues reveals novel regulatory genes in ascorbic acid biosynthesis.PeerJ. 2024 Oct 25;12:e18327. doi: 10.7717/peerj.18327. eCollection 2024. PeerJ. 2024. PMID: 39469594 Free PMC article.
-
Insights into Genes Encoding LEA_1 Domain-Containing Proteins in Cyperus esculentus, a Desiccation-Tolerant Tuber Plant.Plants (Basel). 2024 Oct 19;13(20):2933. doi: 10.3390/plants13202933. Plants (Basel). 2024. PMID: 39458880 Free PMC article.
-
Identification of Multifunctional Putative Bioactive Peptides in the Insect Model Red Palm Weevil (Rhynchophorus ferrugineus).Biomolecules. 2024 Oct 19;14(10):1332. doi: 10.3390/biom14101332. Biomolecules. 2024. PMID: 39456265 Free PMC article.
-
DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms.BMC Bioinformatics. 2024 Oct 24;25(Suppl 2):335. doi: 10.1186/s12859-024-05924-1. BMC Bioinformatics. 2024. PMID: 39448913 Free PMC article.
-
A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks.NPJ Syst Biol Appl. 2024 Oct 24;10(1):124. doi: 10.1038/s41540-024-00448-z. NPJ Syst Biol Appl. 2024. PMID: 39448682 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources
