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
Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids
Guangming He,Xiaopeng Zhu,Axel A. Elling,Liangbi Chen,Xiangfeng Wang,Xiangfeng Wang,Lan Guo,Manzhong Liang,Hang He,Hang He,H Zhang,Fangfang Chen,Yijun Qi,Runsheng Chen,Xing Wang Deng,Xing Wang Deng +15 more
TL;DR: Highly integrated maps of the epigenome, mRNA, and small RNA transcriptomes of two rice subspecies and their reciprocal hybrids reveal that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions.
Journal ArticleDOI
RNA-seq: from technology to biology.
Samuel Marguerat,Jürg Bähler +1 more
TL;DR: Technical issues accompanying RNA-seq data generation and analysis are described, highlighting differences to array-based approaches and recent biological insight gained from applyingRNA-seq and related approaches to deeply sample transcriptomes in different cell types or physiological conditions are reviewed.
Journal ArticleDOI
Inhibition of microRNA function by antimiR oligonucleotides
TL;DR: This review focuses on the use of antisense oligonucleotides (antimiRs) in miRNA inhibition for loss-of-function studies and summarizes recent progress in antimiR mediated pharmacological inhibition of disease-associated miRNAs, which shows great promise in the development of novel miRNA-based therapeutics.
Journal ArticleDOI
Increased inflammatory markers identified in the dorsolateral prefrontal cortex of individuals with schizophrenia
Stu G. Fillman,Stu G. Fillman,Nicole Cloonan,Vibeke S. Catts,Vibeke S. Catts,Linda C. Miller,Jenny Wong,T McCrossin,Murray J. Cairns,Cynthia Shannon Weickert,Cynthia Shannon Weickert +10 more
TL;DR: Changes in an inflammatory response pathway that are present in ∼40% of people diagnosed with schizophrenia are demonstrated, suggesting that therapies aimed at immune system attenuation in schizophrenia may be of direct benefit in the brain.
Journal ArticleDOI
A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling.
Anna V. Klepikova,Artem S. Kasianov,Artem S. Kasianov,Evgeny S. Gerasimov,Evgeny S. Gerasimov,Maria D. Logacheva,Maria D. Logacheva,Maria D. Logacheva,Aleksey A. Penin,Aleksey A. Penin +9 more
TL;DR: The genome-wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing revealed 25 706 protein-coding genes, as well as their stability and their spatiotemporal specificity.
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