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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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Ten years of next-generation sequencing technology.

TL;DR: An overview of the evolution of NGS is provided and the most significant improvements in sequencing technologies and library preparation protocols are discussed and the current landscape of N GS applications is explored to provide a perspective for future developments.
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Understanding mechanisms underlying human gene expression variation with RNA sequencing

TL;DR: It is demonstrated that eQTLs near genes generally act by a mechanism involving allele-specific expression, and that variation that influences the inclusion of an exon is enriched within and near the consensus splice sites.
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Multi-omics approaches to disease.

TL;DR: This review provides an overview of omics technologies and methods for their integration across multiple omics layers and offers the opportunity to understand the flow of information that underlies disease.
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Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads.

TL;DR: A read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation, which results in a higher useable sequence yield and improved accuracy compared to that of existing software.
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CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

TL;DR: It is shown that CEL-Seq gives more reproducible, linear, and sensitive results than a PCR-based amplification method, and will be useful for transcriptomic analyses of complex tissues containing populations of diverse cell types.
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.
Journal ArticleDOI

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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