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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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Long noncoding RNAs in development and disease of the central nervous system

TL;DR: The growing evidence for the importance of lncRNAs in the CNS and the indications that their dysregulation underlies some neurological disorders are highlighted.
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Stability, delivery and functions of human sperm RNAs at fertilization

TL;DR: The diverse and unique attributes of sperm transcripts that were revealed provides the first detailed analysis of the biology and anticipated clinical significance of spermatozoal RNAs.
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RNA-Seq technology and its application in fish transcriptomics.

TL;DR: An overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data is provided and the recent biological insights obtained from the RNA- sequencing studies in a variety of fish species are discussed.
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Burden-driven feedback control of gene expression

TL;DR: This work combined RNA-seq with an in vivo assay to identify the major transcriptional changes that occur in Escherichia coli when inducible synthetic constructs are expressed and built a dCas9-based feedback-regulation system that automatically adjusts the expression of a synthetic construct in response to burden.
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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