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RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang, +2 more
- 01 Jan 2009 - 
- Vol. 10, Iss: 1, pp 57-63
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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.

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Citations
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Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis

TL;DR: The results, including assembled transcriptomes, annotated functional elements and enriched differentially expressed genes amongst different molting stages, provide novel insights into the functions of the hepatopancreas in energy metabolism and biological processes pertaining to molting in crustaceans.
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The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression

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Linnorm: improved statistical analysis for single cell RNA-seq expression data

TL;DR: Linnorm shows advantages in speed, technical noise removal and preservation of cell heterogeneity, which can improve existing methods in the discovery of novel subtypes, pseudo-temporal ordering of cells, clustering analysis, etc.
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A comprehensive, quantitative, and genome-wide model of translation.

TL;DR: A comprehensive and quantitative model of translation was developed, characterising protein synthesis separately for individual genes, and it was implemented in Saccharomyces cerevisiae, and its results were compared with available data, yielding reasonably good correlations.
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GABAergic gene expression in postmortem hippocampus from alcoholics and cocaine addicts; corresponding findings in alcohol-naïve P and NP rats.

TL;DR: This study confirms the involvement of the GABAergic system in alcoholism but also reveals a hippocampal GABA input in cocaine addiction and provides clues to predisposing factors for alcohol and drug addiction.
References
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Journal ArticleDOI

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TL;DR: 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.
PatentDOI

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Mapping short DNA sequencing reads and calling variants using mapping quality scores

TL;DR: This work describes the software MAQ, software that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome, e.g., from a human sample.
Journal ArticleDOI

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

TL;DR: It is found that the Illumina sequencing data are highly replicable, with relatively little technical variation, and thus, for many purposes, it may suffice to sequence each mRNA sample only once (i.e., using one lane).
Journal ArticleDOI

SOAP: short oligonucleotide alignment program

TL;DR: The program SOAP is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology, which supports multi-threaded parallel computing and has a batch module for multiple query sets.
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