GEO DataSets

(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) 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) 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) Here we use RNA sequencing to identify the regulon of the two-component system regulator VirR under normal growth conditions. We generated an in-frame deletion of the virR gene and extracted RNA from this strain grown to mid-log phase in LB as well as the 10403S parental strain. We then analyzed differential expression of transcripts between these two strains using RNA-seq

Organism:

Listeria monocytogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21330

12 Samples

Download data: TXT

(Submitter supplied) The extensively studied intracellular pathogen, L. monocytogenes, is an ideal model for identifying small-molecule agents for treating bacterial infections. By selecting specific biological targets in L. monocytogenes, which are common to Gram-positive pathogens, we could extrapolate drug discovery information derived from this well-studied bacterium. Attenuating the pathogen’s virulence and stress response attributes without killing it, eliminates selective pressure caused by disruption of essential gene functions (as done by current antibiotics) and reduces the likelihood of developing microbes that are impervious to the effects of antibiotics. more...

Organism:

Listeria monocytogenes; Listeria innocua; Listeria monocytogenes 10403S

Type:

Expression profiling by array

Platform:

GPL5029

1 Sample

Download data: GPR

(Submitter supplied) Pseudomonas syringae, the leading cause of crop diseases world-wide, uses type III secretion system (T3SS) to invade host plants. Our previous studies demonstrate that two-component system RhpRS enable P. syringae to coordinate T3SS gene expression, which is dependent on the phosphorylation state of RhpR in different environmental conditions. Homologs of RhpRS are distributed in a wide range of bacterial species, indicating a general regulatory mechanism. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24018

26 Samples

Download data: XLSX

(Submitter supplied) High hydrostatic pressure processing (HPP) is currently being used as a treatment for certain foods to control the presence of food-borne pathogens, such as Listeria monocytogenes. Genomic microarray analysis was performed to determine the effects of HPP on L. monocytogenes in order to understand how it responds to mechanical stress injury. Reverse transcriptase PCR analysis of tufB and rpoC indicated that the reduction of mRNA expression in HPP treated cells was dependent on intensity and time of the treatment. more...

Organism:

Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL5334

9 Samples

Download data: GPR

(Submitter supplied) Comparison of transcriptome of L. monocytogenes EGDe at 24°C and 37°C L. monocytogenes EGDe cells used in this study were grown either at 24°C or 37°C to an OD600 = 0.82-0.87 and the transcriptome of these two conditions was compared

Organism:

Listeria monocytogenes EGD-e

Type:

Expression profiling by array

Platform:

GPL17774

12 Samples

Download data: GPR

(Submitter supplied) Purpose: The objective of the present study was to refine the PrfA regulatory network using RNA-seq to characterize the L. monocytogenes transcriptome in a wt, ∆prfA, and prfA* under PrfA-inducing conditions. Methods: Sequence reads were aligned to the L. monocytogenes 10403S genome using the BWA-MEM algorithm, version 0.7.3a. The data for coverage per base on the sense and antisense strands were analyzed separately using SAMtools. more...

Organism:

Listeria monocytogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26477

9 Samples

Download data: TXT

(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) Microbial population heterogeneity allows for a differential microbial response to environmental stresses and can lead to the selection of stress resistant variants. In this study, we have used two different stress resistant variants of Listeria monocytogenes LO28 with mutations in the rpsU gene encoding ribosomal protein S21, to elucidate features that can contribute to fitness, stress-tolerance and host interaction using a comparative gene profiling and phenotyping approach. more...

Organism:

Listeria monocytogenes; Listeria monocytogenes LO28

Type:

Expression profiling by array

Platform:

GPL25009

10 Samples

Download data: TXT

(Submitter supplied) Analysis of L. monocytogenes ptsH, hprK and ccpA mutants defective in carbon catabolite repression (CCR) control revealed significant alterations in the expression of PrfA-dependent genes. The hprK mutant showed high up-regulation of PrfA-dependent virulence genes upon growth in glucose-containing media whereas expression of these genes was even slightly down-regulated in the ccpA mutant when compared to the wild-type strain. more...

Organism:

Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL4418

10 Samples

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(Submitter supplied) CodY is a nutritional regulator mainly involved in amino acid metabolism. It has been extensively studied in Bacillis subtilis and Lactococcus lactis. We investigated the role of CodY in gene regulation and virulence of the human pathogen Streptococcus pneumoniae. We constructed a codY-mutant and examined the effect on gene and protein expression by microarray and 2D DIGE analysis. The pneumococcal CodY-regulon was found to consist predominantly of genes involved in amino acid metabolism, but also several other cellular processes, such as carbon metabolism and iron uptake. more...

Organism:

Streptococcus pneumoniae TIGR4; Streptococcus pneumoniae

Type:

Expression profiling by array

Platform:

GPL5023

7 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to contribute to the understanding of L. monocytogenes virulence and survival capabilities using global gene expression profiling by means of DNA macroarrays. Keywords: strain comparison; correlation between expression and behaviour

Organism:

Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL2811

24 Samples

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(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) Streptococcus pyogenes (group A Streptococcus, GAS) responds to environmental changes in a manner that results in an adaptive regulation of the transcriptome. Global transcriptional regulators are able to integrate important extracellular and intracellular information and are responsible for modulation of the transcriptional network. The roles of several global transcriptional regulators in adaptation and virulence gene expression have been described. more...

Organism:

Streptococcus pyogenes NZ131

Type:

Expression profiling by array

Platform:

GPL11420

40 Samples

Download data: CEL

(Submitter supplied) Transcriptional profling of a Listeria monocytogenes under pressure comparing ctsR mutant and wild type

Organism:

Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL6489

4 Samples

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(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 630; Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10731

3 Samples

Download data: TXT

(Submitter supplied) The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator HrcA, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DhrcA stationary phase cells were compared to wt to identify hrcA-dependent genes. We identified 61 HrcA-dependent genes that showed significant expression ratios (adj. more...

Organism:

Listeria monocytogenes; Listeria innocua

Type:

Expression profiling by array

Platform:

GPL5029

1 Sample

Download data: GPR

(Submitter supplied) Microarray analyses comparing the transcriptional profile of wild-type EGDe relative to ∆mogR (L. monocytogenes) during growth at 37˚C and RT in BHI broth and during intracellular growth inside J774 host cells at 37˚C. These analyses revealed that MogR primarily functions to repress flagellar motility genes during growth at 37˚C. Keywords: EGDe vs ∆mogR, Temperature, Growth condition

Organism:

Listeria monocytogenes

Type:

Expression profiling by array

Platform:

GPL3074

14 Samples

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