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
Beneficial effects of silicon on salt and drought tolerance in plants
Yongxing Zhu,Haijun Gong +1 more
TL;DR: In this paper, the authors review recent advances on silicon uptake, transport, and accumulation in plants and how silicon alleviates salinity toxicity and drought stress, and the major points are the following: (1) both passive and active silicon uptake may coexist in plants; (2) although silicon transporters have been identified in some plants, the process of silicon transport needs further clarification; (3) the mechanisms for silicon-mediated tolerance of salinity and drought have been extensively investigated at both physiological and biochemical levels.
Journal ArticleDOI
Uncovering the Complexity of Transcriptomes with RNA-Seq
TL;DR: The paper aims to give a survey of the RNA-Seq methodology, particularly focusing on the challenges that this application presents both from a biological and a bioinformatics point of view.
Journal ArticleDOI
Most "dark matter" transcripts are associated with known genes.
TL;DR: Short-read RNA sequencing in mouse and human tissues shows that most transcripts are encoded within or nearby known genes and that most of the genome is not transcribed.
Journal ArticleDOI
The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines.
Decio L. Eizirik,Michael Sammeth,Thomas Bouckenooghe,Guy Bottu,Giorgia Sisino,Mariana Igoillo-Esteve,Fernanda Ortis,Izortze Santin,Maikel Luis Colli,Jenny Barthson,Luc Bouwens,Linda Hughes,Lorna Gregory,Gerton Lunter,Lorella Marselli,Piero Marchetti,Mark I. McCarthy,Mark I. McCarthy,Miriam Cnop +18 more
TL;DR: The present study doubles the number of known genes expressed in human islets and shows that cytokines modify alternative splicing inhuman islet cells, indicating that more than half of the known T1D candidate genes are expressed inHuman islets.
Book ChapterDOI
Analysis of RNA-Seq Data Using TopHat and Cufflinks.
TL;DR: The method of analyzing RNA-Seq data using the set of open source software programs of the Tuxedo suite: TopHat and Cufflinks and an accessory tool called CummeRbund, which processes the output files of Cuffdiff and gives an output of publication quality plots and figures of the user's choice.
References
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