GEO DataSets

(Submitter supplied) The stringent response is characterized by the synthesis of the messenger molecules pppGpp, ppGpp or pGpp (collectively designated (pp)pGpp). The phenotypic consequences resulting from (pp)pGpp accumulation vary among species and can be mediated by different underlying mechanisms. Most genome-wide analyses were performed under stress conditions, which often mask the immediate effects of (pp)pGpp mediated regulatory circuits. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24034

12 Samples

Download data: XLS

(Submitter supplied) The stringent response is initiated by rapid (p)ppGpp synthesis, which leads to a profound reprogramming of gene expression in most bacteria. The stringent phenotype seems to be species specific and may be mediated by fundamentally different molecular mechanisms. In Staphylococcus aureus, (p)ppGpp synthesis upon amino acid deprivation is achieved through the synthase domain of the bifunctional enzyme RSH (RelA/SpoT homolog). more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL10537

12 Samples

Download data: TXT

(Submitter supplied) In the present study we analyzed the response of S. aureus to mupirocin, the drug of choice for nasal decolonization of S. aureus. Mupirocin selectively inhibits the bacterial isoleucyl-tRNA synthetase (IleRSs) leading to the accumulation of uncharged isoleucyl-tRNA and hence (p)ppGpp. The latter is a signal for the induction of the stringent response, an important global transcriptional and translational control mechanism that allows bacteria to adapt to nutritional deprivation. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL13937

4 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling to define the stringent response regulon and significance of basal (p)ppGpp levels in E. faecalis OG1RF.

Organism:

Enterococcus faecalis OG1RF; Enterococcus faecalis

Type:

Expression profiling by array

Platform:

GPL15039

48 Samples

Download data: MEV

(Submitter supplied) In this report, codY mutant strains were constructed and used to demonstrate the relationship of (p)ppGpp synthesized by RelP and RelQ with the activation of CodY. In addition, because CodY has not been studied in S. mutans, we used microarrays to demonstrate that this protein function as a global regulator of gene expression in S. mutans. Keywords: stress response, gene knockout analysis

Organism:

Streptococcus mutans

Type:

Expression profiling by array

Platform:

GPL4340

8 Samples

Download data: MEV

(Submitter supplied) The Staphylococcus aureus accessory gene regulator (agr) is a prototype quorum-sensing system in Gram-positive bacteria and a paradigmatic example of gene regulation by a small regulatory RNA, RNAIII. Using genome-wide transcriptional profiling in the community-associated methicillin-resistant (CA-MRSA) strain MW2, we demonstrate here that in contrast to the current model of target gene regulation by agr, a large subset of agr-regulated genes is controlled independently of RNAIII. more...

Organism:

Coxiella burnetii; Rickettsia rickettsii; Staphylococcus aureus; Staphylococcus epidermidis ATCC 12228; Chlamydia caviae GPIC; Chlamydia pneumoniae AR39; Coxiella burnetii RSA 493; Granulibacter bethesdensis; Borreliella burgdorferi B31; Chlamydia trachomatis D/UW-3/CX; Staphylococcus haemolyticus JCSC1435; Chlamydia muridarum; Staphylococcus epidermidis RP62A; Staphylococcus aureus subsp. aureus MW2

Type:

Expression profiling by array

Platform:

GPL4692

27 Samples

Download data: CEL, CHP

(Submitter supplied) More than 200 direct CodY target genes in Staphylococcus aureus were identified by genome-wide analysis of in vitro DNA binding. This analysis, which was confirmed for some genes by DNase I footprinting assays, revealed that CodY is a direct regulator of numerous transcription units associated with amino acid biosynthesis, transport of macromolecules and virulence. The virulence genes regulated by CodY fell into three groups. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL1339

17 Samples

Download data: CEL, CHP

(Submitter supplied) The production of (p)ppGpp by Streptococcus mutans UA159 is catalyzed by three gene products, RelA, RelP and RelQ. Here, we investigate the role of the RelA (Rel) homologue of S. mutans in the stringent response and in global control of gene expression. RelA of S. mutans was shown to synthesize pppGpp in vitro from GTP and ATP in the absence of added ribosomes, as well as in vivo in an E. coli relA-spoT mutant. more...

Organism:

Streptococcus mutans

Type:

Expression profiling by array

Platform:

GPL4340

16 Samples

Download data: MEV

(Submitter supplied) We sequenced a total of 16 cDNA libararies derived from fragmented total mRNA and ribosome protected mRNAs from S. aureus hpf mutant (NE838) and its parental strain JE2 grown in tryptic soy broth (TSB) or minimal medium (MM). The data represented 2 independent biological replicates.

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17452

16 Samples

Download data: TXT

(Submitter supplied) Microarray expression profiling of S. aureus lavaged from murine lungs after residence times between 30 minutes and 6 hours compared to post-exponential phase or early log phase growth in Luria-Betani broth.

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL4047

21 Samples

Download data: CEL

(Submitter supplied) Bacterial and eukaryotic cells survive an otherwise lethal heat shock once they are primed by a mild pre-heat shock. Using B. subtilis as a model organism, we investigated transcriptional changes during thermotolerance development at 37 °C, 48 °C, 53 °C and 48/53 °C and observed a comprehensive upregulation of genes of the general and heat shock response and the downregulation of many translation-related genes. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18561

32 Samples

Download data: CSV, FNA, GFF, RPKM, TAB

(Submitter supplied) Changes in Enterococcus faecalis OG1RF(pCF10) gene expression at 4 hours post-infection in a rabbit model of subdermal abscess formation were studied using RNA-seq analysis.

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18799

2 Samples

Download data: TXT

(Submitter supplied) Changes in Enterococcus faecalis OG1RF gene expression during infection in a rabbit model of subdermal abscess formation were studied using microarray analysis.

Organism:

Enterococcus faecalis OG1RF; Enterococcus faecalis V583

Type:

Expression profiling by array

Platform:

GPL10534

12 Samples

Download data: TXT

(Submitter supplied) With a copy number of about 25,000 molecules per cell, Asp23 is one of the most abundant proteins in Staphylococcus aureus. Asp23 has been characterized as a protein with an apparent molecular mass of 23 kDa that, following an alkaline shock, accumulates in the soluble protein fraction. Moreover, it was shown that transcription of the asp23 gene is exclusively regulated by the alternative sigma factor B. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL7137

12 Samples

Download data: TXT

(Submitter supplied) Staphylococcus aureus is a leading cause of hospital- and community-associated infections. The organism’s ability to cause disease can, in part, be attributable to its ability to adapt to otherwise deleterious host-associated stresses. Like other bacterial species, the modulation of mRNA turnover appears to play an important role in S. aureus adaptation to certain environmental stresses. In the current study Affymetrix GeneChips® were used to examine the S. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by array

Platform:

GPL1339

30 Samples

Download data: CEL, CHP