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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
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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Computational approaches to disease‐gene prediction: rationale, classification and successes

TL;DR: A basic classification scheme for computational approaches to disease‐gene prediction is developed and applied to exhaustively review bioinformatics tools that have been developed for this purpose, focusing on conceptual aspects rather than technical detail and performance.
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Whole-transcriptome brain expression and exon-usage profiling in major depression and suicide: evidence for altered glial, endothelial and ATPase activity.

TL;DR: Results lend further support for models in which deficits in microglial, endothelial (blood–brain barrier), ATPase activity and astrocytic cell functions contribute to MDD and suicide, and identify putative pathways and mechanisms for further study in these disorders.
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Next-generation sequencing technologies: An overview.

TL;DR: A review of short-read and long-read sequencing technologies can be found in this paper, where the authors provide an overview of these technologies as two paradigms: short read and long read.
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UGT genomic diversity: beyond gene duplication

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Accelerated recruitment of new brain development genes into the human genome.

TL;DR: Systematic transcriptional profiling across human and mouse revealed that evolutionarily young genes are overrepresented in the developing (fetal and infant) human neocortex.
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

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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