title: RNA-Seq: a method for comprehensive transcriptome analysis.
abstract: A recently developed technique called RNA Sequencing (RNA-Seq) uses massively parallel sequencing to allow transcriptome analyses of genomes at a far higher resolution than is available with Sanger sequencing- and microarray-based methods. In the RNA-Seq method, complementary DNAs (cDNAs) generated from the RNA of interest are directly sequenced using next-generation sequencing technologies. The reads obtained from this can then be aligned to a reference genome in order to construct a whole-genome transcriptome map. RNA-Seq has been used successfully to precisely quantify transcript levels, confirm or revise previously annotated 5' and 3' ends of genes, and map exon/intron boundaries. This unit describes protocols for performing RNA-Seq using the Illumina sequencing platform.
authors.affiliation: Molecular, Cellular, and Developmental Biology Department, Yale University, New Haven, Connecticut, USA.
authors.forename: Ugrappa
authors.initials: U
authors.lastname: Nagalakshmi
authors.forename: Karl
authors.initials: K
authors.lastname: Waern
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
mesh_terms: D018076:DNA, Complementary / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary