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Genome Biol DOI:10.1186/gb-2012-13-3-r23

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

Publication TypeJournal Article
Year of Publication2012
AuthorsGiannoukos, G, Ciulla, DM, Huang, K, Haas, BJ, Izard, J, Levin, JZ, Livny, J, Earl, AM, Gevers, D, Ward, DV, Nusbaum, C, Birren, BW, Gnirke, A
JournalGenome Biol
Date Published2012
KeywordsChemical Fractionation, DNA, Complementary, Escherichia coli, Feces, Gene Expression Regulation, Bacterial, High-Throughput Nucleotide Sequencing, Humans, Microbial Consortia, Prochlorococcus, Rhodobacter sphaeroides, RNA, Bacterial, RNA, Messenger

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.


Alternate JournalGenome Biol.
PubMed ID22455878
PubMed Central IDPMC3439974
Grant ListAI-076608 / AI / NIAID NIH HHS / United States
CA139193 / CA / NCI NIH HHS / United States
HHSN272200900018C / / PHS HHS / United States
U54 HG004969 / HG / NHGRI NIH HHS / United States