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
GC-content normalization for RNA-Seq data.
TL;DR: The authors' within-lane normalization procedures, followed by between-lanenormalization, reduce GC-content bias and lead to more accurate estimates of expression fold-changes and tests of differential expression.
Journal ArticleDOI
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Franck Rapaport,Raya Khanin,Yupu Liang,Mono Pirun,Azra Krek,Paul Zumbo,Christopher E. Mason,Nicholas D. Socci,Doron Betel +8 more
TL;DR: A large number of computational methods have been developed for analyzing differential gene expression in RNA-seq data as discussed by the authors, and a comprehensive evaluation of common methods using the SEQC benchmark dataset and ENCODE data.
Journal ArticleDOI
Origins, evolution, and phenotypic impact of new genes
TL;DR: The origin and evolution of new genes and their functions in eukaryotes is reviewed, demonstrating that novel genes of the various types significantly impacted the evolution of cellular, physiological, morphological, behavioral, and reproductive phenotypic traits.
Comprehensive comparative analysis of strand-specific RNA sequencing methods
Joshua Z. Levin,Moran Yassour,Moran Yassour,Xian Adiconis,Chad Nusbaum,Dawn Thompson,Nir Friedman,Andreas Gnirke,Aviv Regev +8 more
TL;DR: A comprehensive computational pipeline is developed to compare library quality metrics from any RNA-seq method and identified the dUTP second-strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the current availability of paired-end sequencing.
Journal ArticleDOI
Single-cell RNA-seq: advances and future challenges
TL;DR: An overview of the biological questions single-cell RNA-seq has been used to address, the major findings obtained from such studies, and current challenges and expected future developments in this booming field are provided.
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