Open Access Highly Accessed Research article

The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression

Vinoy K Ramachandran1†, Neil Shearer1†, Jobin J Jacob1, Cynthia M Sharma2 and Arthur Thompson1*

1 Institute of Food Research, Norwich, UK, University of Würzburg, Josef-Schneider-Str. 2/Bau D15, 97080 Würzburg, Germany

2 Research Center for Infectious Diseases (ZINF), University of Würzburg, Josef-Schneider-Str. 2/Bau D15, 97080 Würzburg, Germany

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BMC Genomics 2012, 13:25 doi:10.1186/1471-2164-13-25

Published: 17 January 2012

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Additional file 1:

Supplementary Tables (S1, S2, S3, S4). Table S1: Mapping statistics for wild-type and ΔrelAΔspoT libraries. Table S2: Primers used for 5' RACE identification of TSSs. Table S3: Comparison of published Salmonella TSSs and dRNA-seq TSSs. Table S4: Probes and primers used for detection of ncRNAs.

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Additional file 2:

Supplementary Tables S1, S2, S3, S4, S5, S6, S7, S8, S9. Table S1: Master table of TSSs and ppGpp-dependent expression levels for S. Typhimurium SL1344 ORFs. Table S2: Leaderless transcripts. Table S3: TSSs and ppGpp-dependent expression of known and predicted small RNAs. Table S4: TSSs and ppGpp-dependent expression of new candidate small RNAs. Table S5: TSSs and ppGpp-dependent expression of candidate antisense RNAs. Table S6: TSSs and ppGpp-dependent expression rRNAs and tRNAs. Table S7: Predicted new ORFs. Table S8: Comparison of ppGpp-dependent expression from microarray and dRNA-seq data. Table S9: Re-annotated ORFs.

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Additional file 3:

Supplementary Figures S1, S2, S3, S4, S5, S6, S7, S8, S9. Figure S1: 5' RACE identification of transcriptional start sites. Figure S2: Functional category analysis of 1932 promoters of annotated SL1344 ORFs that contain a predicted -10 motif. Figure S3: Functional category analysis of 1932 promoters of annotated SL1344 ORFs that contain a predicted -10 and -35 motif. Figure S4: Functional category analysis of 264 promoters of annotated SL1344 ORFs that contain conserved motif 1. Figure S5: Northern Blot detection of non-coding RNAs. Figure S6: Adapter assisted PCR detection of asRNAs. Figure S7: Functional category analysis of ORFs opposite to candidate asRNAs. Figure S8: Growth curves for S. Typhimurium SL1344 wild-type ΔrelAΔspoT strains. Figure S9: Invasion of S. Typhimurium SL1344 wild-type and isogenic ΔrelAΔspoT strains in HeLa cells at 2 h and intracellular replication at 6 h post-infection.

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