RNA-Seq: a revolutionary tool for transcriptomics
Reads0
Chats0
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.read more
Citations
More filters
Journal ArticleDOI
Transcriptomic responses of the softwood-degrading white-rot fungus Phanerochaete carnosa during growth on coniferous and deciduous wood
Jacqueline MacDonald,Matt Doering,Thomas Canam,Yunchen Gong,David S. Guttman,Malcolm M. Campbell,Emma R. Master +6 more
TL;DR: Gene set enrichment analyses did not distinguish transcriptomes resulting from softwood and hardwood cultivations, suggesting that similar sets of enzyme activities are elicited by P. carnosa grown on different wood substrates, albeit to different expression levels.
Journal ArticleDOI
SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing.
Armando Geraldes,Johnson Pang,Nina Thiessen,Timothee Cezard,Richard D. Moore,Yongjun Zhao,Angela Tam,Shucai Wang,Michael Friedmann,Inanc Birol,Steven J.M. Jones,Quentin C. B. Cronk,Carl J. Douglas +12 more
TL;DR: The results of the sequencing of the transcriptome of developing xylem in 20 accessions with high‐throughput next generation sequencing technology suggest that the current annotation of the poplar genome is remarkably incomplete and that there are many transcripts and novel genes waiting to be annotated.
Journal ArticleDOI
Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review
TL;DR: This review aims to summarize the contemporary understanding and findings with regard to infectious pathogens and the immune system of fish that have been achieved through RNA-Seq technology.
Journal ArticleDOI
Statistical significance for hierarchical clustering
TL;DR: In this article, a Monte Carlo based approach for testing statistical significance in hierarchical clustering is proposed, which is implemented as a sequential testing procedure guaranteeing control of the family-wise error rate.
References
More filters
Journal ArticleDOI
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
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
Kenneth W. Kinzler,Victor Velculescu,Bert Vogelstein,Lin Zhang,ヴェルヴレスク,ヴィクター,イー.,ヴォゲルステイン,バート,キンズラー,ケネス,ダブリュ.,ツァン,リン +7 more
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
Heng Li,Jue Ruan,Richard Durbin +2 more
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.
Related Papers (5)
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred Grabherr,Brian J. Haas,Moran Yassour,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Lin Fan,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nicholas Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Nir Friedman,Aviv Regev +22 more