Journal ArticleDOI
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
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TLDR
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.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 × 10 5 distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices. The mRNA population specifies a cell’s identity and helps to govern its present and future activities. This has made transcriptome analysis a general phenotyping method, with expression microarrays of many kinds in routine use. Here we explore the possibility that transcriptome analysis, transcript discovery and transcript refinement can be done effectively in large and complex mammalian genomes by ultra-high-throughput sequencing. Expression microarrays are currently the most widely used methodology for transcriptome analysis, although some limitations persist. These include hybridization and cross-hybridization artifacts 1–3 , dye-based detection issues and design constraints that preclude or seriously limit the detection of RNA splice patterns and previously unmapped genes. These issues have made it difficult for standard array designs to provide full sequence comprehensiveness (coverage of all possible genes, including unknown ones, in large genomes) or transcriptome comprehensiveness (reliable detection of all RNAs of all prevalence classes, including the least abundant ones that are physiologically relevant). Otherread more
Citations
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Journal ArticleDOI
Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq
Guoqin Liu,Guoqin Liu,Wanshun Li,Penghua Zheng,Tong Xu,Lijuan Chen,Dongfeng Liu,Sayed Hussain,Yuanwen Teng +8 more
TL;DR: The new transcriptomes offer comprehensive sequence and DGE profiling data for a dynamic view of transcriptomic variation during bud dormancy in pear and provided a basis for future studies of metabolism during bud college in non-model but economically-important perennial species.
Journal ArticleDOI
Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.
TL;DR: This work uses publicly available mouse data to perform a joint analysis of genomic and proteomic data obtained on the same organism and observes that spectral count based protein abundance metrics are comparable to intensity based measures with respect to correlation with gene expression data.
Journal ArticleDOI
Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow
Jochen B. W. Wolf,Till Bayer,Bernhard Haubold,Markus Schilhabel,Philip Rosenstiel,Diethard Tautz +5 more
TL;DR: A clear clustering of expression profiles is found for the pure carrion crow animals and disperse profiles for the animals from the hybrid zone, suggesting that gene expression differences may indeed be a sensitive indicator of initial species divergence.
Book ChapterDOI
Differential Expression Analysis of Complex RNA-seq Experiments Using edgeR
TL;DR: The statistical theory underlying the edgeR software package for differential expression of RNA-seq data is reviewed, which uses weighted likelihood methods to implement a flexible empirical Bayes approach in the absence of easily tractable sampling distributions.
Journal ArticleDOI
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
TL;DR: A systematic comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species and an increase in both the false-negative rate and thefalse-positive rate for lowly expressed genes are reported.
References
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PatentDOI
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TL;DR: Serial analysis of gene expression (SAGE) should provide a broadly applicable means for the quantitative cataloging and comparison of expressed genes in a variety of normal, developmental, and disease states.
Journal ArticleDOI
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Ugrappa Nagalakshmi,Zhong Wang,Karl Waern,C. Shou,Debasish Raha,Mark Gerstein,Michael Snyder +6 more
TL;DR: A quantitative sequencing-based method is developed for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome, and it is demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed.
Journal ArticleDOI
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
Ryan Lister,Ronan C. O'Malley,Julian Tonti-Filippini,Brian D. Gregory,Charles C. Berry,A. Harvey Millar,Joseph R. Ecker +6 more
TL;DR: Deep sequencing of smRNAs revealed a direct relationship between the location of sm RNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylisation, and a tendency for smRN as to direct strand-specific DNA methylations in regions of RNA-DNA homology.
Journal ArticleDOI
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
Philipp Kapranov,Jill Cheng,Sujit Dike,David A. Nix,Radharani Duttagupta,Aarron T. Willingham,Peter F. Stadler,Jana Hertel,Jörg Hackermüller,Ivo L. Hofacker,Ian Bell,Evelyn Cheung,Jorg Drenkow,Erica Dumais,Sandeep Patel,Gregg Helt,Madhavan Ganesh,Srinka Ghosh,Antonio Piccolboni,Victor Sementchenko,Hari Tammana,Thomas R. Gingeras +21 more
TL;DR: Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes and support a highly interleaved organization of the human transcriptome.
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