RNA-Seq: a revolutionary tool for transcriptomics
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TLDR
The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.Abstract:
RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.read more
Citations
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Journal ArticleDOI
Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data
Emma M. Quinn,Paul Cormican,Elaine Kenny,Matthew Hill,Richard Anney,Michael Gill,Aiden Corvin,Derek W. Morris +7 more
TL;DR: The best method to achieve high specificity and sensitivity, and greatest number of SNP calls, is to remove duplicate sequence reads after alignment to the genome and to call SNPs using SAMtools.
Journal ArticleDOI
RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression
Emilie Lalonde,Kevin C.H. Ha,Zibo Wang,Amandine Bemmo,Claudia L. Kleinman,Tony Kwan,Tomi Pastinen,Jacek Majewski +7 more
TL;DR: High correlation between the levels of mature and unprocessed RNA is demonstrated, implying that ∼75% of eQTL target variance can be explained by control at the level of transcription, but that the remaining 25% may be regulated co- or post-transcriptionally.
Journal ArticleDOI
Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress.
Lei Lei,Junpeng Shi,Jian Chen,Mei Zhang,Silong Sun,Shaojun Xie,Xiaojie Li,Biao Zeng,Lizeng Peng,Andrew Hauck,Haiming Zhao,Weibin Song,Zaifeng Fan,Jinsheng Lai +13 more
TL;DR: This study indicates that plant can respond to drought stress with highly dynamic translational mechanism, that acting synergistically with that of transcription.
Journal ArticleDOI
The Escherichia coli transcriptome mostly consists of independently regulated modules
Anand V. Sastry,Ye Gao,Richard Szubin,Ying Hefner,Sibei Xu,Donghyuk Kim,Donghyuk Kim,Kumari Sonal Choudhary,Laurence Yang,Laurence Yang,Zachary A. King,Bernhard O. Palsson,Bernhard O. Palsson +12 more
TL;DR: Unsupervised machine learning is applied to a diverse compendium of over 250 high-quality Escherichia coli RNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets and finds that most gene sets represent the effects of specific transcriptional regulators.
Journal ArticleDOI
Characterizing natural variation using next-generation sequencing technologies
TL;DR: A better understanding of the sources of error and bias in sequencing data is essential, especially in the context of studies of variation at dynamic quantitative traits.
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