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Tiling array hybridizations of genomic DNA from Staphylococcus aureus HG001.

ABSTRACT: This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (Mäder, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different bilogical conditions. Genomic DNA was prepared from four independent cultures of S. aureus HG001 cells; after sonication, DNA was labeled with Cy3 and hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift.

ORGANISM(S): Staphylococcus aureus subsp. aureus NCTC 8325 Staphylococcus aureus

PROVIDER: GSE70042 | GEO | 2016/03/08

SECONDARY ACCESSION(S): PRJNA287529

REPOSITORIES: GEO

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Tiling array hybridizations of genomic DNA from Staphylococcus aureus HG001.

Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (MÃ¤der, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different bilogical conditions. Genomic DNA was prepared from four independent cultures of S. aureus HG001 cells; after sonication, DNA was labeled with Cy3 and hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift. genomic DNA from wild type

2016-03-08 | E-GEOD-70042 | biostudies-arrayexpress

Tiling array hybridizations of genomic DNA from Bacillus subtilis 168.

Project description:Genomic DNA prepared from B. subtilis 168 cells grown to stationary phase was hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347). B. subtilis 168 was grown in LB medium to stationary phase. Genomic DNA was prepared from four independent cultures. After sonication, DNA was labeled with Cy3 and hybridized to tiling arrays.

2012-03-07 | E-GEOD-27419 | biostudies-arrayexpress

Tiling array hybridizations of genomic DNA from Bacillus subtilis 168.

2012-03-07 | GSE27419 | GEO

Transcriptome analysis of a Staphylococcus aureus mutant defective in the transcription termination factor Rho.

Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (Mäder, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different biological conditions. The data revealed a relatively low abundance of antisense RNAs in S. aureus, overlapping only 6% of the coding genes. Transcriptome analysis of the rho deletion mutant revealed a remarkable overall increase in antisense transcription in S. aureus.

2016-03-08 | GSE70041 | GEO

Transcriptome analysis of a Staphylococcus aureus mutant defective in the transcription termination factor Rho.

Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (MÃ¤der, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different biological conditions. The data revealed a relatively low abundance of antisense RNAs in S. aureus, overlapping only 6% of the coding genes. Transcriptome analysis of the rho deletion mutant revealed a remarkable overall increase in antisense transcription in S. aureus. delta rho and wild type

2016-03-08 | E-GEOD-70041 | biostudies-arrayexpress

Staphylococcus aureus HG001

Project description:Staphylococcus aureus HG001

| PRJNA287528 | ENA

Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions

Project description:We report the condition-dependent transcriptome of S. aureus HG001, a derivative of strain NCTC 8325, by strand-specific tiling array hybridizations. More than 40 experimental conditions were investigated ranging from optimal in vitro growth to interaction with host cells. Analyses included the systematic mapping of transcription units, annotation of non-coding RNAs, the classification of promoters according to their dependency on SigA and SigB, and the prediction of potentially new transcription factor target sites. Antisense RNAs being of particular interest because of the small number of alternative sigma factors used by S. aureus were found to be relatively rare, overlapping only 6% of the annotated coding genes. RNA samples prepared from S. aureus HG001 grown in shake flask or cell culture infection experiments were reverse transcribed, labeled and hybridized to tiling arrays. Hybridizations were performed in triplicate using RNA isolated from independent cultures.

2016-03-08 | E-GEOD-70040 | biostudies-arrayexpress

Exoproteome profiling reveals the involvement of the foldase PrsA in the cell surface properties and pathogenesis of S. aureus

Project description:Staphylococcus aureus is a bacterial pathogen that produces and exports many virulence factors that cause human diseases. PrsA, a membrane-bound foldase that is found ubiquitously in Gram-positive bacteria, is required for the folding of exported proteins into a stable and active structure. However, the involvement of PrsA in post-translocational protein folding in S. aureus remains unclear. In this study, a PrsA-deficient mutant of S. aureus HG001 was constructed and prsA deletion was shown to enhance auto-aggregation and increase the ability of S. aureus HG001 to adhere to human lung epithelial cells. The lack of PrsA made the bacteria more sensitive to sonication-induced lysis. In a mouse infection model, mice that were infected with a prsA-knockout strain HG001ΔprsA had a higher survival rate than those infected with the wild-type strain. An iTRAQ-based quantitative exoproteome analysis was conducted to identify the proteins whose secretion was affected by PrsA. The exoproteomic analysis revealed that prsA deletion altered the amounts of several proteins that were related to the properties of the cell surface and virulence. These include proteins involved in cellular adhesion and cell wall synthesis such as extracellular adhesion protein (Eap), undecaprenyl-diphosphatase (UppP) and FmtA, and proteins involved in subverting host innate immunity such as immunoglobulin-binding proteins Spa and Sbi, chemotaxis inhibitory protein (CHIP) and staphylococcal complement inhibitor (SCIN). The results of this study suggested that PrsA is required for the post-translocational folding of many exported proteins and critically affects the cell surface properties and pathogenesis of S. aureus.

2018-01-24 | PXD008528 | Pride

Activity of SigB Modulates Virulence Gene Expression in a Murine Staphylococcus aureus Infection Model but Does Not Influence the Host Kidney Gene Expression

Project description:Background. Infections caused by Staphylococcus aureus are associated with significant morbidity and mortality and are an increasing threat not only in hospital settings. The expression of the staphylococcal virulence factor repertoire is known to be affected by the alternative sigma factor B (SigB). However, its impact during infection still is a matter of debate. Methods. Kidney tissue of controls or mice infected with S. aureus HG001 or its isogenic sigB mutant was analyzed by transcriptome profiling to monitor the host response, and additionally expression of selected S. aureus genes was monitored by RT-qPCR. Results. Direct transcript analysis by RT-qPCR revealed significant SigB activity in all mice infected with the wild type strain (WT), but not in its isogenic sigB mutant (p<0.0001). Despite a clear cut difference in the SigB-dependent transcription pattern of virulence genes (clfA, aur, and hla), the host reaction to infection (either WT or sigB mutant) was almost identical. Conclusions. Despite its significant activity in vivo, loss of SigB did not have an effect on the outcome of infection as well as on murine kidney gene expression pattern. Thus, these data support the role of SigB as virulence modulator rather than being a virulence determinant by itself. Murine kidney gene expression pattern of 3 groups were compared: 1) after infection with S. aureus HG001 (wild type); 2) after infection with S. aureus HG001 ΔsigB; 3) sham control (injection of physiological saline solution). The infection was performed twice (2 biological replicates), and the array analysis included 4 or 5 mice (independent samples) per group. In total, the study consisted of 24 arrays.

2011-10-23 | E-GEOD-28540 | biostudies-arrayexpress

Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions

2016-03-08 | GSE70040 | GEO