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

Georgia Giannoukos1*, Dawn M Ciulla1, Katherine Huang1, Brian J Haas1, Jacques Izard2,3, Joshua Z Levin1, Jonathan Livny1, Ashlee M Earl1, Dirk Gevers1, Doyle V Ward1, Chad Nusbaum1, Bruce W Birren1 and Andreas Gnirke1

1 Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, 320 Charles Street and 301 Binney Street, Cambridge, MA 02141, USA

2 Department of Molecular Genetics, The Forsyth Institute, 245 First Street, Cambridge, MA 02142, USA

3 Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, 188 Longwood Ave, Boston, MA 02115, USA

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Genome Biology 2012, 13:r23 doi:10.1186/gb-2012-13-3-r23

Published: 28 March 2012

Additional files

Additional file 1:

Figures S1 through S8 and legends. Figure S1: linear correlation of gene expression profiles before and after different rRNA depletion methods. Figure S2: detrimental effect of high GC content on enrichment by low-c0t normalization using duplex specific nuclease (DSN). Figure S3: fragmentation profile of total RNA prior to Ribo-Zero treatment. Figure S4: PER CDS detection sensitivity before and after Ribo-Zero treatment of intact and fragmented RNA. Figure S5: antisense read densities for two technical replicates of strand-specific RNA seq of Ribo-zero treated PER RNA. Figure S6: representation of bacterial species in sequencing data sets from two human stool samples. Figure S7: RNA-seq data for Prevotella copri, Bacteroides vulgatus, and Eubacterium rectale in stool A. Figure S8: RNA-seq data for Prevotella copri and Bacteroides vulgatus in stool B.

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Additional file 2:

List of 649 reference genomes with GenBank accession numbers.

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Additional file 3:

Total mapped reads to top 19 species in stool samples.

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Additional file 4:

List of unannotated rRNAs in stool samples.

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Additional file 5:

Sample recovery through the RNA-seq process assessed by the Agilent Bioanalyzer RNA 6000 Pico and DNA High Sensitivity Kits.

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Additional file 6:

RNA-seq metrics and Sequence Read Archive accession numbers.

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