GEO DataSets

(Submitter supplied) We performed differential RNA-seq of two Staphylococcus epidermidis clinical isolates (PS2 and PS10) to compare their transcription profiles. The isolates were originally obtained from blood cultures during a systemic infection in an immunocompromised patient (Weisser et al. 2010. J Clin Microbiol 48: 2407-2412). They are of clonal origin, but differ phenotypically with respect to extracellular biofilm matrix production. more...

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26150

4 Samples

Download data: WIG

(Submitter supplied) Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in stationary phase (10 h). Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in stationary phase (10 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. more...

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23256

9 Samples

Download data: XLSX

(Submitter supplied) Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in log-phase (6 h) Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in log-phase (6 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. more...

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23256

9 Samples

Download data: GFF, XLS

(Submitter supplied) Background: Staphylococcus epidermidis (SE) has emerged as one of the most important causes of nosocomial infections. The SaeRS two-component signal transduction system (TCS) influences virulence and biofilm formation in Staphylococcus aureus. The deletion of saeR in S. epidermidis results in impaired anaerobic growth and decreased nitrate utilization. However, the regulatory function of SaeRS on biofilm formation and autolysis in S. more...

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by array

Platform:

GPL13532

12 Samples

Download data: TXT

(Submitter supplied) Biofilm formation is considered the most important factor involved in pathogenicity of Staphylococcus epidermidis.We investigated the role of two-component signal transduction system (TCS) srrAB, which was up-regulated under micro-aerobic condition, in the growth and biofilm formation of S. epidermidis.AsrrA-deficient mutant (∆srrA) derived from S. epidermidis1457 (SE1457), exhibited dramatic reduction in growth and biofilm formation underboth aerobic and micro-aerobic conditions, and more sensitive to several different types of antimicrobial agents, H2O2 and SDS. more...

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by array

Platform:

GPL13532

18 Samples

Download data: TXT

(Submitter supplied) To explain enhanced biofilm formation and increased dissemination of S. epidermidis in mixed-species biofilms, microarrays were used to explore differential gene expression of S. epidermidis in mixed-species biofilms. One sample from single species biofilm (S1) and mixed-species biofilm (SC2) were excluded from analyses for outliers. We observed upregulation (2.7%) and down regulation (6%) of S. epidermidis genes in mixed-species biofilms. more...

Organism:

Candida albicans; Staphylococcus epidermidis RP62A; Staphylococcus epidermidis

Type:

Expression profiling by array

Platform:

GPL15175

4 Samples

Download data: GPR

(Submitter supplied) To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development we constructed and characterized codY ccpA double mutant in S. aureus UAMS-1.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28116

24 Samples

Download data: XLSX

(Submitter supplied) The custom-made S. epidermidis GeneChips(Shanghai Biochip Co., Ltd) included qualifiers representing open reading frame (ORF) sequences identified in the genomes of the S. epidermidis strain RP62A, as well as unique ORFs in S. epidermidis strain 12228. The GeneChips were composed of cDNA array containing PCR products of 2316 genes and oligonucleotide array containing 252 genes.Two-component regulatory systems (TCSs) play a pivotal role in bacterial adaptation, survival, and virulence by sensing changes in the external environment and modulating gene expression in response to a variety of stimuli.To investigate the regulatory role of LytSR, one of the TCSs identified in the genomes of S. more...

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by array

Platforms:

GPL10140 GPL10141

7 Samples

Download data: TXT

(Submitter supplied) The 70-mers oligo sequences were designed by Operon based on Staphylococcus epidermidis strain RP62A genome sequence from TIGR. Each oligo was printed twice on slides.

Organism:

Staphylococcus epidermidis

Download data

(Submitter supplied) We sequenced mRNA from three independent biological replicates of Staphylococcus epidermidis biofilms with different proportion of dormant cells.

Organism:

Staphylococcus epidermidis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17893

6 Samples

Download data: TXT

(Submitter supplied) Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated-annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. more...

Organism:

Staphylococcus aureus; Staphylococcus epidermidis; Staphylococcus carnosus

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21408 GPL19476 GPL21407

3 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL16057 GPL24214

14 Samples

Download data

(Submitter supplied) Bacterial regulatory RNAs (sRNA) generally act by base-pairing with target mRNAs. While identification of sRNA targets is the essential step in sRNA characterization, it remains a stumbling block in most studies. To study sRNA-regulated networks in the major human pathogen Staphylococcus aureus, we used a RNA-RNA interactome screening method for identifying sRNA targets based on synthetic sRNAs that are used in vitro as bait to trap their corresponding targets. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24214

10 Samples

Download data: TXT

(Submitter supplied) Bacterial regulatory RNAs (sRNA) generally act by base-pairing with target mRNAs. While identification of sRNA targets is the essential step in sRNA characterization, it remains a stumbling block in most studies. To study sRNA-regulated networks in the major human pathogen Staphylococcus aureus, we used a RNA-RNA interactome screening method for identifying sRNA targets based on synthetic sRNAs that are used in vitro as bait to trap their corresponding targets. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16057

4 Samples

Download data: CSV, GFF

(Submitter supplied) The SaeRS two-component regulatory system of Staphylococcus aureus is known to affect the expression of many genes. The SaeS protein is the histidine kinase responsible for phosphorylation of the response regulator SaeR. In S. aureus Newman, the sae system is constitutively expressed due to a point mutation in saeS, relative to other S. aureus strains, which results in substitution of proline for leucine at amino acid 18. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18481

10 Samples

Download data: TXT

(Submitter supplied) Biofilms are surface-adhered bacterial communities encased in an extracellular matrix composed of polysaccharides, proteins, and extracelluar (e)DNA, with eDNA being required for the formation and integrity of biofilms. Here we demonstrate that the spatial and temporal release of eDNA is regulated by BfmR, a regulator essential for Pseudomonas aeruginosa biofilm development. The expression of bfmR coincided with localized cell death and DNA release, with high eDNA concentrations localized to the outer part of microcolonies in the form of a ring and as a cap on small clusters. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

6 Samples

Download data: CEL, CHP

(Submitter supplied) Analysis of the intergenic regions of Staphylococcus aureus by bioinformatics predicted multiple regulatory regions. From this analysis, we also characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. more...

Organism:

Staphylococcus aureus; Staphylococcus aureus subsp. aureus NCTC 8325; Staphylococcus aureus subsp. aureus N315; Staphylococcus aureus subsp. aureus USA300; Staphylococcus aureus subsp. aureus Mu50; Staphylococcus aureus subsp. aureus MSSA476; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus COL; Staphylococcus aureus subsp. aureus MW2

Type:

Non-coding RNA profiling by array

Platform:

GPL7137

2 Samples

Download data: TXT

(Submitter supplied) We have studied the transcriptome of S. aureus SH1000 strain, isogenic Teg49 mutant strain, and isogenic plasmid complemented strain

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24034

6 Samples

Download data: CSV

(Submitter supplied) The profiles of transcripts from the planktonic cells and biofilm cells of V. vulnificus were compared by using a V. vulnificus whole-genome microarray

Organism:

Vibrio vulnificus; Vibrio vulnificus CMCP6

Type:

Expression profiling by array

Platform:

GPL17798

6 Samples

Download data: TXT

(Submitter supplied) In this work we have demonstrated increased mutability of Staphylococcus aureus and S. epidermidis in biofilms and have explored the mechanisms underlying the enhanced mutability. A novel static biofilm model, utilising cellulose filter disks, was developed to support the formation of mature biofilms with sufficiently high cell densities to permit determination of mutation frequencies. The mutability of biofilm cultures increased up to 60 fold and 4 fold for S. more...

Organism:

Staphylococcus aureus; Staphylococcus aureus subsp. aureus NCTC 8325

Type:

Expression profiling by array

Platform:

GPL15230

9 Samples

Download data: CALLS, PAIR