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Genome Biol. 2012;13(3):R23. doi: 10.1186/gb-2012-13-3-r23.

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

Author information

1
Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA. ggiannou@broadinstitute.org

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.

PMID:
22455878
PMCID:
PMC3439974
DOI:
10.1186/gb-2012-13-3-r23
[Indexed for MEDLINE]
Free PMC Article

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