RNA-Seq: a revolutionary tool for transcriptomics
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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
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Journal ArticleDOI
Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems.
TL;DR: An overview of N GS technologies that are currently available and the bioinformatics analyses that are necessary to obtain information from the flood of sequencing data as well as applications of NGS to address biological questions in eukaryotic microorganisms are provided.
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microRNAs and genetic diseases
TL;DR: An overview of the evidence available to date which support the pathogenic role of miRNAs in human genetic diseases is provided, and the results of recent studies indicating the phenotypic consequences of miRNA alterations on the function of several tissues and organs are suggested.
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Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant ( Camellia sinensis )
Chun Fang Li,Yan Zhu,Yao Yu,Qiongyi Zhao,Qiongyi Zhao,Sheng Jun Wang,Xinchao Wang,Ming Zhe Yao,Da Luo,Xuan Li,Liang Chen,Yajun Yang +11 more
TL;DR: The data revealed the possible critical check points in the flavonoid, caffeine, and theanine biosynthesis pathways, but also implicated the key transcription factors and related mechanisms in the regulation of secondary metabolite biosynthesis.
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RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis
TL;DR: The use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain a comprehensive overview of the H. brasiliensis transcriptome is reported, providing the most comprehensive sequence resource available for the study of rubber trees as well as demonstrates effective use of Illumina sequencing and deNovo transcriptsome assembly in a species lacking genomic information.
Journal ArticleDOI
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
MacIntosh Cornwell,Mahesh Vangala,Len Taing,Zachary T. Herbert,Johannes Köster,Johannes Köster,Bo Li,Hanfei Sun,Taiwen Li,Jian Zhang,Xintao Qiu,Matthew Pun,Rinath Jeselsohn,Myles Brown,X. Shirley Liu,Henry W. Long +15 more
TL;DR: VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion.
References
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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.
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