Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis


This web-page provides access to the supplementary tables in Microsoft Excel format that are referred to in the Supplementary Online Material of our publication "Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis" (Nicolas, Mäder, Dervyn et al., submitted).

We also reference in the second section the other links related to this data set including a version of the Supplementary Online Material with high resolution supplementary figures.

1. Supplementary tables

Table Location Description
Table S1MS Excel file List of the growth conditions used for the 269 mRNA profiling experiments
Table S2MS Excel file Expression levels for all features in the 269 mRNA profiling experiments
Table S3MS Excel file Least and most expressed genes in all conditions
Table S4MS Excel file List of promoter up-shifts with cluster information and TU definition
Table S5MS Excel file Information summary for each feature
Table S6MS Excel file Analysis of newly annotated RNA features
Table S7MS Excel file List of high confidence down-shifts and classification
Table S8MS Word file Summary of the repertoire of down-shifts
Table S9MS Excel file List of 3' extended mRNAs in the rho knock-out mutant
Table S10MS Excel file Genome-wide effects on antisense transcription upon Rho inactivation
Table S11MS Excel file List of all sense-antisense RNA pairs detected in wild-type
Table S12MS Word file Classification of core promoters
Table S13MS Word file Correspondence between unsupervised promoter classification and sigma factor binding sites from DBTBS
Table S14MS Word file Summary of sigma factor-dependency of novel RNA features

2. Other links

SOM file

A high definition version Figure S21: Expression of the genes involved in the main metabolic pathways across conditions.

Transcriptome browser

Transcriptome profiles for the wild-type and the rho-mutant can be browsed here.

Unsupervised clustering of promoter sequences

The source code of the software that we have developped for unsupervised clustering of the promoter sequence data based on bipartite motifs can be downloaded here.

GEO records

Link Description Reviewer link
GSE27219 Data from the 269 BsubT1 tiling array mRNA measurements of the wild-type strain For review
GSE27303 Data from the BsubT2 tiling array mRNA measurements to assess the role of Rho For review
GSE27419 Genomic-DNA hybridizations to assess probe-specific affinities in the BsubT2 tiling array For review
GSE27652 Data from the SigA ChIP-Chip experiments For review

Openbis record

Summarized expression values of all RNA features across the 269 tiling array mRNA measurements of the wild-type strain are also available in the Openbis database (navigate to "Experiment -> Browser", go to the RE-ANNOTATION Project and select the Experiment).

For review: connect with user name "" and password "guest".