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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.

SUBMITTER: Giannoukos G

PROVIDER: S-EPMC3439974 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes.

Giannoukos Georgia G Ciulla Dawn M DM Huang Katherine K Haas Brian J BJ Izard Jacques J Levin Joshua Z JZ Livny Jonathan J Earl Ashlee M AM Gevers Dirk D Ward Doyle V DV Nusbaum Chad C Birren Bruce W BW Gnirke Andreas A

Genome biology 20120101 3

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 represe ...[more]

PMID: 22455878

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