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
High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases
Yidan Qin,Jun Yao,Douglas C. Wu,Ryan M. Nottingham,Sabine Mohr,Scott Patrick Hunicke-Smith,Alan M. Lambowitz +6 more
TL;DR: A new RNA-seq method that exploits thermostable group II intron reverse transcriptases (TGIRTs) and used it to profile human plasma RNAs, revealing RNA fragments mapping to a diverse population of protein-coding gene and long ncRNAs, as well as nearly all known classes of small ncRNA species, some of which have never before been seen in plasma.
Journal ArticleDOI
Single Nucleotide Polymorphism Discovery in Cultivated Tomato via Sequencing by Synthesis
John P. Hamilton,Sung Chur Sim,Kevin Stoffel,Allen Van Deynze,C. Robin Buell,David M. Francis +5 more
TL;DR: The transcript sequences and the annotated SNPs provide a resource to facilitate tomato genetics and breeding efforts and the utility of these SNPs for assessing genetic variation within cultivated and wild populations was demonstrated.
Journal ArticleDOI
Mendelian and Non-Mendelian Regulation of Gene Expression in Maize
Lin Li,Katherine Petsch,Rena Shimizu,Sanzhen Liu,Wayne Wenzhong Xu,Kai Ying,Jianming Yu,Michael J. Scanlon,Patrick S. Schnable,Marja C.P. Timmermans,Nathan M. Springer,Gary J. Muehlbauer +11 more
TL;DR: Along with genes showing Mendelian inheritance in the RIL population, there are also genes whose expression level and variation in the progeny could not be predicted based on parental difference, indicating that non-Mendelian factors also contribute to expression variation.
Journal ArticleDOI
Functional genomics of adaptation to hypoxic cold-stress in high-altitude deer mice: Transcriptomic plasticity and thermogenic performance
TL;DR: In each experimental group, highland mice exhibited greater thermogenic capacities than lowland mice, and this enhanced performance was associated with upregulation of transcriptional modules that influence several hierarchical steps in the O2 cascade, including tissue O2 diffusion (angiogenesis) and tissue O1 utilization (metabolic fuel use and cellular oxidative capacity).
Journal ArticleDOI
Metabolomics, peptidomics and proteomics applications of capillary electrophoresis-mass spectrometry in Foodomics: A review
TL;DR: The aim of this review work is to present an overview of the most recent developments and applications of CE-MS as analytical platform for Foodomics, covering the relevant works published from 2008 to 2012.
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