title: Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.
abstract: We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We applied this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical stool samples. The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA.
authors.affiliation: Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA. ggiannou@broadinstitute.org
authors.forename: Georgia
authors.initials: G
authors.lastname: Giannoukos
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Ciulla
authors.forename: Katherine
authors.initials: K
authors.lastname: Huang
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: Jacques
authors.initials: J
authors.lastname: Izard
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.forename: Jonathan
authors.initials: J
authors.lastname: Livny
authors.forename: Ashlee M
authors.initials: AM
authors.lastname: Earl
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.forename: Doyle V
authors.initials: DV
authors.lastname: Ward
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.forename: Andreas
authors.initials: A
authors.lastname: Gnirke
mesh_terms: D005591:Chemical Fractionation; D018076:DNA, Complementary / Q000032:analysis / Q000096:biosynthesis; D004926:Escherichia coli / Q000235:genetics*; D005243:Feces / Q000382:microbiology; D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D059013:Microbial Consortia / Q000235:genetics*; D048929:Prochlorococcus / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics*; D012333:RNA, Messenger / Q000032:analysis / Q000096:biosynthesis; D012242:Rhodobacter sphaeroides / Q000235:genetics*
chemical_list: D018076:DNA, Complementary; D012329:RNA, Bacterial; D012333:RNA, Messenger