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
Genome Wide Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Sclerotinia sclerotiorum Infection in Brassica napus.
TL;DR: Quantitative RT-PCR verification of a set of S. sclerotiorum responsive sense/antisense transcript pairs revealed contrasting expression patterns, supporting the hypothesis that steric clashes of transcriptional machinery may lead to inactivation of sense promoter, and highlighting the potential contributions of lncRNAs in regulating expression of plant genes that respond to biotic stress.
Journal ArticleDOI
Two methods for full-length RNA sequencing for low quantities of cells and single cells
Xinghua Pan,Russell E. Durrett,Haiying Zhu,Yoshiaki Tanaka,Yumei Li,Xiaoyuan Zi,Sadie L. Marjani,Ghia Euskirchen,Chao Ma,Chao Ma,Robert H. LaMotte,In-Hyun Park,Michael Snyder,Christopher E. Mason,Sherman M. Weissman +14 more
TL;DR: These protocols for the amplification and high-throughput sequencing of very small amounts of RNA for sequencing using procedures of either semirandom primed PCR or phi29 DNA polymerase-based DNA amplification, for the cDNA generated with oligo-dT and/or random oligonucleotide primers are reported.
Journal ArticleDOI
Empirical comparison of cross-platform normalization methods for gene expression data
Jason Rudy,Faramarz Valafar +1 more
TL;DR: Of the four successful methods, XPN generally shows the highest inter-platform concordance when treatment groups are equally sized, while DWD is most robust to differently sized treatment groups and consistently shows the smallest loss in gene detection.
Journal ArticleDOI
Emerging Targeted Therapy for Tumors with NTRK Fusion Proteins.
Ed Kheder,David S. Hong +1 more
TL;DR: The potential oncogenic characteristics of TRK fusion proteins in various malignancies are discussed and ongoing clinical trials of kinase inhibitors targeting them are highlighted.
Journal ArticleDOI
Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
Gaye Lightbody,Valeriia Haberland,Fiona Browne,Laura E. Taggart,Huiru Zheng,Eileen Parkes,Jaine K. Blayney +6 more
TL;DR: An up-to-date overview of the evolution of HTS and the accompanying tools, infrastructure and data management approaches that are emerging in this space, which, if used within in a multidisciplinary context, may ultimately facilitate the development of personalized medicine.
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