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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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Subcellular transcriptomics—Dissection of the mRNA composition in the axonal compartment of sensory neurons

TL;DR: A novel organ culture system is presented, which enables the isolation of RNA specifically from NGF dependent re‐growing peripheral axons of mouse embryo, sensory neurons, and it is found that the axon is enriched in mRNAs that encode secreted proteins, transcription factors, and the translation machinery.
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Drug discovery in advanced prostate cancer: translating biology into therapy

TL;DR: The evolving therapeutic landscape of CRPC is reviewed and issues associated with precision medicine as well as challenges encountered with immunotherapy for this disease are discussed.
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Simultaneous transcriptional profiling of bacteria and their host cells.

TL;DR: An RNA-Seq-based method to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with intracellular bacteria is developed and discovered a possible chlamydial strategy for early iron acquisition, putative immune dampening effects of chlamYDial infection on the host cell, and a hypothesis for Chlamydia-induced fibrotic scarring through runaway positive feedback loops.
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Helper T‐cell differentiation and plasticity: insights from epigenetics

TL;DR: Recent progress in the understanding of how cytokines influence gene expression and epigenetic modifications is discussed, and the impact of these findings on the authors' views of helper cell lineage commitment and plasticity is discussed.
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

Serial analysis of gene expression

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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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