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We began analyzing https://www.nature.com/articles/nmeth.1226, but it redirected us to https://www.nature.com/articles/nmeth.1226. The analysis below is for the second page.

Title[redir]:
Mapping and quantifying mammalian transcriptomes by RNA-Seq | Nature Methods
Description:
The mouse transcriptome in three tissue types has been analyzed using Illumina next-generation sequencing technology. This quantitative RNA-Seq methodology has been used for expression analysis and splice isoform discovery and to confirm or extend reference gene models. Also in this issue, another paper reports application of the ABI SOLiD technology to sequence the transcriptome in mouse embryonic stem cells. 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.

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article, google, scholar, nature, cas, supplementary, gene, methods, access, content, analysis, data, genome, rna, science, cookies, information, mouse, expression, microarrays, nat, privacy, sequencing, references, splicing, bmc, transcriptome, author, mapping, rnaseq, mortazavi, williams, wold, genes, liver, alternative, online, research, human, myers, biol, biology, dataset, permissions, advertising, subscribe, published, mammalian, transcriptomes, ali,

Topics {✒️}

nature portfolio transcriptome research permissions reprints professional data handling privacy policy advertising nature social media lorian schaeffer & barbara wold development author correspondence rna-seq ali mortazavi rna-seq analyses reveal springerlink instant access remaining data suggest pre-mrna splicing nih training grant alternative mrna splicing transcriptomic analyses reveal single nucleotide resolution full-length transcriptome rna splice events rna maps reveal gene expression methods transcriptional landscape privacy personal data supplementary methods van de peer rna-binding proteins permissions skeletal muscle tissues genome tiling arrays journals search log rare mrna sequences differentially expressed genes yeast genome defined genome-wide survey reduced genome strains exon junction microarrays data protection preliminary data european economic area quantifying mammalian transcriptomes previously unknown genes candidate microrna precursors institutional subscriptions read replacing crna targets tag-based approaches human transcribed sequences

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