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
Inference of Isoforms from Short Sequence Reads
Jianxing Feng,Wei Li,Tao Jiang +2 more
TL;DR: A method to calculate the expression levels of isoforms and infer isoforms from short RNA-Seq reads using exon-intron boundary, transcription start site (TSS) and poly-A site (PAS) information and an efficient algorithm (called IsoInfer) to search for isoforms is proposed.
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Comparative Transcriptome Analysis of Cultivated and Wild Watermelon during Fruit Development.
Shaogui Guo,Honghe Sun,Haiying Zhang,Jingan Liu,Yi Ren,Guoyi Gong,Chen Jiao,Yi Zheng,Wencai Yang,Zhangjun Fei,Zhangjun Fei,Yong Xu +11 more
TL;DR: Comparison of transcriptome profiles of fruit tissues of cultivated watermelon 97103 and wild watermelon PI296341-FR provided novel insights into watermelon fruit quality and ripening biology and found that genes in the ethylene biosynthesis and signaling pathway showed highly ripening-associated expression patterns, indicating a possible role of ethylene in fruit development and ripens of watermelon, a non-climacteric fruit.
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Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species
Diana Bellin,Alberto Ferrarini,Antonio Chimento,Olaf Kaiser,Natasha Levenkova,Pascal Bouffard,Massimo Delledonne +6 more
TL;DR: An innovative approach based on 454 sequencing of 3' cDNA fragments from a normalized library constructed from pooled RNAs to generate a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence is not available, which can be used for large scale analysis of gene expression in any species.
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The role of alternative splicing in cancer: From oncogenesis to drug resistance.
Rocco Sciarrillo,Anna Wojtuszkiewicz,Yehuda G. Assaraf,Gerrit Jansen,Gertjan J.L. Kaspers,Elisa Giovannetti,Jacqueline Cloos +6 more
TL;DR: An extensive overview of the latest findings in the field of regulation of splicing in cancer, including molecular mechanisms by which cancer cells harness alternative splicing to drive oncogenesis and evade anticancer drug treatment as well as splicing-based vulnerabilities that can provide novel treatment opportunities are provided.
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Dark Matter RNA: Existence, Function, and Controversy
TL;DR: The mysteries surrounding the ∼97–98% of the human genome that does not encode proteins have long captivated imagination of scientists, and this question could be referred to without much exaggeration as the most important issue in genetics today.
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