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
Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes
Rebecca M. Davidson,Candice N. Hansey,Malali Gowda,Kevin L. Childs,Haining Lin,Brieanne Vaillancourt,Rajandeep S. Sekhon,Rajandeep S. Sekhon,Natalia de Leon,Natalia de Leon,Shawn M. Kaeppler,Shawn M. Kaeppler,Ning Jiang,C. Robin Buell +13 more
TL;DR: The data and analyses in this study provide valuable tools through improved gene annotation, gene family characterization, and a core set of candidate genes to further characterize maize reproductive development and improve grain yield potential.
Journal ArticleDOI
The Coding and Noncoding Architecture of the Caulobacter crescentus Genome
Jared M. Schrader,Bo Zhou,Gene-Wei Li,Keren Lasker,W. Seth Childers,Brandon Williams,Tao Long,Sean Crosson,Harley H. McAdams,Jonathan S. Weissman,Lucy Shapiro +10 more
TL;DR: Overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach, providing a valuable genomic resource to elucidate the complete C. crescentus genetic circuitry that controls asymmetric cell division.
Journal ArticleDOI
Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations.
TL;DR: Common experimental approaches to SNP calling are summarized, highlighting recent polyploid successes and a series of best practices for SNP calling in polyploids are proposed.
Journal ArticleDOI
De Novo Assembly and Characterization of the Transcriptome of the Parasitic Weed Dodder Identifies Genes Associated with Plant Parasitism
Aashish Ranjan,Yasunori Ichihashi,Moran Farhi,Kristina Zumstein,Brad T. Townsley,Rakefet David-Schwartz,Neelima Sinha +6 more
TL;DR: Transcriptional dynamics during parasitism in the parasitic weed Cuscuta pentagona reveals increased expression of genes encoding transporters and stimulus response regulators, and a decrease in the expression of photosynthetic proteins.
Journal ArticleDOI
Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum
Evelien M. Bunnik,Duk-Won D. Chung,Michael Hamilton,Nadia Ponts,Nadia Ponts,Anita Saraf,Jacques Prudhomme,Laurence Florens,Karine G. Le Roch +8 more
TL;DR: Different layers of translational regulation are likely to contribute to a complex network that controls gene expression in this eukaryotic pathogen, and disrupting the mechanisms involved in such translational control could provide novel anti-malarial strategies.
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