GEO DataSets

(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) 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) To gain knowledge on L. monocytogenes differential CodY activity, we set on analyzing CodY’s regulon in L. monocytogenes in both rich and minimal growth conditions using genome wide sequencing techniques. Remarkably, we identified for the first time a global regulatory role for CodY when BCAAs are limited, that are similar to those within the mammalian niche. Furthermore, our data establish CodY as a central regulator that integrates metabolism, motility, stress responses and virulence in L. more...

Organism:

Listeria monocytogenes

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21330

8 Samples

Download data: XLSX

(Submitter supplied) To gain knowledge on L. monocytogenes differential CodY activity, we set on analyzing CodY’s regulon in L. monocytogenes in both rich and minimal growth conditions using genome-wide sequencing techniques. Remarkably, we identified for the first time a global regulatory role for CodY when BCAAs are limited, that are similar to those within the mammalian niche. Furthermore, our data establish CodY as a central regulator that integrates metabolism, motility, stress responses and virulence in L. more...

Organism:

Listeria monocytogenes 10403S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20912

11 Samples

Download data: XLSX

(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) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

24 Samples

Download data: CEL

(Submitter supplied) CodY is a conserved regulator in gram-positive organisms described to repress metabolic genes mainly involved in nitrogen metabolism but also to control the expression of virulence genes in pathogens. We constructed codY gene-replacement mutants in three unrelated S. aureus strains (Newman, UAMS-1, RN1HG). codY mutants grew slower in a chemically defined medium compared to the wild type strains. However, only codY mutants were able to grow in medium lacking threonine. more...

Organism:

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

Type:

Non-coding RNA profiling by array

Platform:

GPL7137

8 Samples

Download data

(Submitter supplied) CodY is a conserved broad acting transcriptional factor that regulates the expression of genes related to amino acid metabolism and virulence in Staphylococcus aureus. CodY target genes have been studied by using in vitro DNA affinity purification and deep sequencing (IDAP-Seq). In this study we performed the first in vivo determination of CodY target genes using a novel CodY monoclonal antibody in established ChIP-exo protocols. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25144

4 Samples

Download data: CSV

(Submitter supplied) Staphylococcus aureus is a major opportunistic pathogen and notable efforts are currently under way to develop new methods to combat staphylococcal infections. It is becoming increasingly clear that understanding the ecology of pathogenic bacteria is important to design improved disinfection and therapeutic strategies. Like many microbes, S. aureus commonly forms biofilms on various biotic and abiotic surfaces. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17452

6 Samples

Download data: TXT

(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) 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) CodY, a global regulatory protein that monitors the nutrient sufficiency of the environment by responding to the intracellular levels of GTP and the branched-chain amino acids, was previously shown to be a potent repressor of toxin gene expression in Clostridium difficile during growth in rich medium. In the intestinal tract, such derepression of toxin synthesis may lead to destruction of epithelial cells and the liberation of potential nutrients for the bacterium. more...

Organism:

Clostridioides difficile; Clostridioides difficile 630

Type:

Expression profiling by array

Platform:

GPL10731

3 Samples

Download data: TXT

(Submitter supplied) Mycobacteria encode several additional alternative ribosomal proteins (AltRP) and the funtion of AltRP invovling in translation is little known. In this study, we investigate the different translation landscape of AltRibo and CanRibo and found AltRibo have a relative 5' reads accumlation and preferential codon usage.

Organism:

Mycolicibacterium smegmatis

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26255

16 Samples

Download data: TXT

(Submitter supplied) Virulence of many bacterial pathogens, including the important human pathogen Staphylococcus aureus, depends on the secretion of frequently high amounts of toxins. Toxin production involves the need for the bacteria to make physiological adjustments for energy conservation. While toxins are primarily known to be targets of gene regulation, such changes may be accomplished by regulatory functions of the toxins themselves. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL4692

12 Samples

Download data: CEL, CHP

(Submitter supplied) Intracellular small-molecule signaling has drawn increasing attention due to its importance in bacterial physiology and host-pathogen interactions. Here, we show that a new quinone-sensing transcriptional regulator, QsbR (quinone-stress sensing and bleomycin resistance regulator), is important for bacterial stress response and virulence in S. aureus. The mutant strain of qsbR exhibits dramatically reduced staphylococcal virulence in a murine abscess model of infection. more...

Organism:

Staphylococcus aureus; Staphylococcus aureus subsp. aureus str. Newman

Type:

Expression profiling by array

Platform:

GPL10597

4 Samples

Download data: MEV

(Submitter supplied) Adaptation and survival in response to diverse stressors involve reprogramming of mRNA translation. Although the cellular response to mild stress has been intensively studied, the response to severe stress remains unclear. We show here that under severe stress conditions, cells induce transient hibernation-like mechanisms in anticipation of recovery, which we have termed the Adaptive Pausing Response (APR). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13112

36 Samples

Download data: TXT

(Submitter supplied) Impairment of translation can lead to stalling and collision of ribosomes which constitute an activation platform for several ribosomal stress-surveillance pathways. Among these is the Ribotoxic Stress Response (RSR), where ribosomal sensing by the MAP3K ZAKa leads to activation of p38 and JNK kinases. Despite these insights, the physiological ramifications of ribosomal impairment and downstream RSR signaling remain elusive. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL24247

4 Samples

Download data: DAT, SGA

(Submitter supplied) To investigate the effect of conditions of culture on gene expression in Vibrio cholerae N16961 We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 conditions of culture in biological duplicate

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30088

8 Samples

Download data: XLSX

(Submitter supplied) We study gene expression levels of V. cholerae N16961 hapR+ corrected strain in exponential phase without and with indole or tobramycin.

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30088

9 Samples

Download data: TXT