Overview
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 S1 | MS Excel file | List of the growth conditions used for the 269 mRNA profiling experiments |
| Table S2 | MS Excel file | Expression levels for all features in the 269 mRNA profiling experiments |
| Table S3 | MS Excel file | Least and most expressed genes in all conditions |
| Table S4 | MS Excel file | List of promoter up-shifts with cluster information and TU definition |
| Table S5 | MS Excel file | Information summary for each feature |
| Table S6 | MS Excel file | Analysis of newly annotated RNA features |
| Table S7 | MS Excel file | List of high confidence down-shifts and classification |
| Table S8 | MS Word file | Summary of the repertoire of down-shifts |
| Table S9 | MS Excel file | List of 3' extended mRNAs in the rho knock-out mutant |
| Table S10 | MS Excel file | Genome-wide effects on antisense transcription upon Rho inactivation |
| Table S11 | MS Excel file | List of all sense-antisense RNA pairs detected in wild-type |
| Table S12 | MS Word file | Classification of core promoters |
| Table S13 | MS Word file | Correspondence between unsupervised promoter classification and sigma factor binding sites from DBTBS |
| Table S14 | MS 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 "reviewer@reannotation.ch" and password "guest".