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
BookDOI
Advanced techniques in diagnostic microbiology
Yi-Wei Tang,Charles W. Stratton +1 more
TL;DR: This paper presents a review of Molecular Techniques for Sexually Transmitted Dieseases Diagnosis, a Multiplex Assay Platform with Applications in Diagnostic Microbiology, and Molecular Differential Diagnoses of Infectious Diseases.
Journal ArticleDOI
RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure
Chen Gao,Shuxun Ren,Jae-Hyung Lee,Jinsong Qiu,Douglas J. Chapski,Christoph Rau,Yu Zhou,Maha Abdellatif,Astushi Nakano,Thomas M. Vondriska,Xinshu Xiao,Xiang-Dong Fu,Jau-Nian Chen,Yibin Wang +13 more
TL;DR: Regulation of RNA splicing by RBFox1 is identified as an important player in transcriptome reprogramming during heart failure that influence pathogenesis of the disease.
Journal ArticleDOI
Cancer genome-sequencing study design
Jill Mwenifumbo,Marco A. Marra +1 more
TL;DR: This Review discusses how aspects of study design and methodological considerations — such as the size and composition of the discovery cohort — can be tailored to serve specific research aims.
Journal ArticleDOI
Next-generation sequencing (NGS) in the microbiological world : how to make the most of your money
TL;DR: The goal of this review is to give an overview of the process, from sample to analysis, and discuss how to optimize your resources to achieve the most from your NGS-based research.
Journal ArticleDOI
SNP genotyping and population genomics from expressed sequences – current advances and future possibilities
TL;DR: This review summarizes current methods, identifies ways that using expressed sequence data benefits population genomic inference and explores how current practitioners evaluate and overcome challenges that are commonly encountered.
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