Staphylococcus aureus transcriptome architecture: from laboratory to infection-mimicking conditions


This web-page provides access to the supplementary tables in Microsoft Excel format that are referred to in the Supporting Information of our publication "Staphylococcus aureus transcriptome architecture: from laboratory to infection-mimicking conditions" (Mäder, Nicolas et al., submitted).

We also reference in the second section the other links related to this data set.

Throughout this document we refer to our S. aureus HG001 as the wild-type. This strain is a close derivative of the widely used model strain S. aureus NCTC 8325 and we use the corresponding Genbank record (CP000253) as the reference sequence and annotation.

1. Supporting tables

Table Link Description
Table Ain SOM text Oligonucleotides used for preparation of Northern blot probes
Table Bin SOM text Comparison of potential trans-encoded small regulatory RNAs with sRNAs identified by previous studies
Table Cin SOM text Known 5’ cis-acting regions of S. aureus
Table Din SOM text Results from previous transcriptome studies in comparison with the SigB regulon revealed by the promoter classification
Table Ein SOM text Target prediction for the potential sRNA S596
Table S1MS Excel file Expression levels for all annotated genes and new RNA features in the 156 RNA samples
Table S2MS Excel file Least and most expressed genes in all conditions
Table S3MS Excel file Correlation coefficients and loadings associated with PCA axes 1-15
Table S4MS Excel file Differential expression analysis of infection-mimicking and antibiotic conditions
Table S5MS Excel file List of promoter up-shifts with cluster information and TU definition
Table S6MS Excel file Information summary for each annotated gene and new RNA feature
Table S7MS Excel file List of high confidence down-shifts and effects of rho deletion at termination sites
Table S8MS Excel file List of promoter up-shifts with transcription factor binding site information
Table S9MS Excel file Transcription factor regulons including previously known and newly identified potential target genes.
Table S10MS Excel file List of up-regulated regions in the Δrho mutant
Table S11MS Excel file List of genes showing differential expression in the Δrho mutant compared to the wild-type

2. Other links

Supporting Figure

Figure S1: Barplots of expression profiles of 47 virulence-associated genes (PDF).

Transcriptome browser

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

GEO records

Link Description Reviewer link
GSE70043 The GEO SuperSeries grouping all the tiling array data of this study;
composed of the SubSeries GSE70040, GSE70041 and GSE70042
For review
GSE70040 Data from the 156 tiling array mRNA measurements of the wild-type strain For review
GSE70041 Data from the 16 tiling array mRNA measurements to assess the role of Rho For review
GSE70042 Data from the 4 tiling array genomic DNA hybridizations to assess probe affinity For review