title: Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.
abstract: Sequence-based methods for transcriptome characterization have typically relied on generation of either serial analysis of gene expression tags or expressed sequence tags. Although such approaches have the potential to enumerate transcripts by counting sequence tags derived from them, they typically do not robustly survey the majority of transcripts along their entire length. Here we show that massively parallel sequencing of randomly primed cDNAs, using a next-generation sequencing-by-synthesis technology, offers the potential to generate relative measures of mRNA and individual exon abundance while simultaneously profiling the prevalence of both annotated and novel exons and exon-splicing events. This technique identifies known single nucleotide polymorphisms (SNPs) as well as novel single-base variants. Analysis of these variants, and previously unannotated splicing events in the HeLa S3 cell line, reveals an overrepresentation of gene categories including those previously implicated in cancer.
authors.affiliation: Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada.
authors.forename: Ryan
authors.initials: R
authors.lastname: Morin
authors.forename: Matthew
authors.initials: M
authors.lastname: Bainbridge
authors.forename: Anthony
authors.initials: A
authors.lastname: Fejes
authors.forename: Martin
authors.initials: M
authors.lastname: Hirst
authors.forename: Martin
authors.initials: M
authors.lastname: Krzywinski
authors.forename: Trevor
authors.initials: T
authors.lastname: Pugh
authors.forename: Helen
authors.initials: H
authors.lastname: McDonald
authors.forename: Richard
authors.initials: R
authors.lastname: Varhol
authors.forename: Steven
authors.initials: S
authors.lastname: Jones
authors.forename: Marco
authors.initials: M
authors.lastname: Marra
mesh_terms: D018076:DNA, Complementary / Q000235:genetics*; D005091:Exons; D020869:Gene Expression Profiling; D006367:HeLa Cells; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012326:RNA Splicing; D012333:RNA, Messenger / Q000032:analysis; D024363:Transcription Initiation Site
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger