RNA-Seq: a revolutionary tool for transcriptomics
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
Power analysis and sample size estimation for RNA-Seq differential expression
TL;DR: A power analysis tool is provided that captures the dispersion in the data and can serve as a practical reference under the budget constraint of RNA-Seq experiments and confirm a local optimal power is achievable for a given budget constraint.
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Confronting false discoveries in single-cell differential expression.
Jordan W. Squair,Jordan W. Squair,Jordan W. Squair,Matthieu Gautier,Matthieu Gautier,Claudia Kathe,Claudia Kathe,Mark Anderson,Mark Anderson,Nicholas D. James,Nicholas D. James,Thomas H. Hutson,Thomas H. Hutson,Rémi Hudelle,Rémi Hudelle,Taha Qaiser,Kaya J.E. Matson,Quentin Barraud,Quentin Barraud,Ariel J. Levine,Gioele La Manno,Michael A. Skinnider,Michael A. Skinnider,Michael A. Skinnider,Grégoire Courtine,Grégoire Courtine +25 more
TL;DR: This article showed that the relative performance of these methods is contingent on their ability to account for variation between biological replicates, and that the most widely used methods can discover hundreds of differentially expressed genes in the absence of biological differences.
Journal ArticleDOI
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
Jeffrey Martin,Jeffrey Martin,Vincent M. Bruno,Zhide Fang,Xiandong Meng,Xiandong Meng,Matthew J. Blow,Matthew J. Blow,Tao Zhang,Tao Zhang,Gavin Sherlock,Michael Snyder,Zhong Wang,Zhong Wang +13 more
TL;DR: Rnnotator as mentioned in this paper is an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome, and it has been applied to two yeast transcriptomes and compared the results to the reference gene catalogs.
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Viral pathogen discovery.
TL;DR: Genomic approaches for pathogen discovery, including consensus polymerase chain reaction (PCR), microarrays, and unbiased next-generation sequencing (NGS), have the capacity to comprehensively identify novel microbes present in clinical samples and are successful in rapidly identifying emerging outbreak threats.
Journal ArticleDOI
Experimental approaches for the discovery and characterization of regulatory small RNA.
Cynthia M. Sharma,Jörg Vogel +1 more
TL;DR: The available toolbox for wet lab-based research, including in vivo and in vitro reporter systems, genetic methods and biochemical co-purification of sRNA interaction partners are reviewed.
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