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Open AccessJournal ArticleDOI

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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What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species

TL;DR: It is proposed that a unified theory of speciation will take into account the idiosyncratic features of genomic architecture examined in the light of each organism’s biology and ecology drawn from across the full breadth of the Tree of Life.
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Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi

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Sexual plasticity: A fishy tale

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Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing.

TL;DR: The collective data generated in the present research represent a valuable resource for further genetic and molecular studies in celery.
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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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.
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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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