GEO DataSets

(Submitter supplied) The transcriptional factor ToxR initiates a virulence regulatory cascade required for V. cholerae to express critical host colonization factors and cause disease. Genome-wide expression studies suggest that ToxR regulates many genes important for V. cholerae pathogenesis, yet our knowledge of the direct regulon controlled by ToxR is limited to just four genes. Here, we determine ToxR’s genome-wide DNA-binding profile and show that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands encoding the majority of V. more...

Organism:

Vibrio cholerae O1 str. C6706

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15333

3 Samples

Download data: TXT

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

Organism:

Vibrio cholerae O1 str. C6706

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15333

7 Samples

Download data: TXT

(Submitter supplied) The transcriptional factor ToxR initiates a virulence regulatory cascade required for V. cholerae to express critical host colonization factors and cause disease. Genome-wide expression studies suggest that ToxR regulates many genes important for V. cholerae pathogenesis, yet our knowledge of the direct regulon controlled by ToxR is limited to just four genes. Here, we determine ToxR’s genome-wide DNA-binding profile and show that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands encoding the majority of V. more...

Organism:

Vibrio cholerae O1 str. C6706

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15333

3 Samples

Download data: TXT

(Submitter supplied) The transcriptional factor ToxR initiates a virulence regulatory cascade required for V. cholerae to express critical host colonization factors and cause disease. Genome-wide expression studies suggest that ToxR regulates many genes important for V. cholerae pathogenesis, yet our knowledge of the direct regulon controlled by ToxR is limited to just four genes. Here, we determine ToxR’s genome-wide DNA-binding profile and show that ToxR is a global regulator of both progenitor genome-encoded genes and horizontally acquired islands encoding the majority of V. more...

Organism:

Vibrio cholerae O1 str. C6706

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15333

3 Samples

Download data: TXT

(Submitter supplied) Vibrio cholerae is a Gram negative, motile, facultative anaerobic bacterium, and the causative agent of cholera, a severe diarrhoeal disease, which untreated can rapidly lead to dehydration, hypotensive shock, and death. Cholera is a significant human disease that is estimated to affect 3-5 million people each year. The mechanism by which V. cholerae regulates virulence gene expression in vivo is unknown, but a number of studies have suggested that low molecular weight signally molecules may be important in modulating gene expression. more...

Organism:

Vibrio cholerae; Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by array

Platform:

GPL15619

4 Samples

Download data: MEV

(Submitter supplied) Cholera is a diarrheal disease caused by Vibrio cholerae of serogroups O1 and O139 that affects impoverished populations worldwide. The histone-like nucleoid structuring protein (H-NS) is a global regulator of environmentally-regulated gene expression that plays a fundamental role in V. cholerae adaptation to disparate ecological niches. We used RNA-seq to characterize the hns transcriptome of El Tor biotype V. more...

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19265

8 Samples

Download data: TXT, XLS

(Submitter supplied) We identified the mutated gene locus in a pigment overproducing Vibrio cholerae mutant of strain A1552. The deduced gene product is suggested to be a oxidoreductase based on partial homology to putative homogentisate 1,2-dioxygenase in Pseudomonas aeruginosa and Mesorhizobium loti and we propose that the gene VC1345 in the V. cholerae genome be denoted hmgA in accordance with the nomenclature for other species. more...

Organism:

Vibrio cholerae

Type:

Expression profiling by array

Platform:

GPL8044

10 Samples

Download data

(Submitter supplied) Transcriptional profiling of Vibrio Cholerae RpoE deletion mutant in toxSL33S mutation background

Organism:

Vibrio cholerae; Vibrio cholerae O395

Type:

Expression profiling by array

Platform:

GPL20849

4 Samples

Download data: DAT

(Submitter supplied) Purpose: to characterize the regulatory targets of an AraC-like transcriptional regulator (VC0513) encoded on the Vibrio Seventh Pandemic Island -II (VSP-II) in V. cholerae O1 El Tor N16961 Methods: RNA was isolated from a wild-type N16961 carrying an IPTG-inducible copy of vc0513, vc0515, or an empty vector control Results: vc0513 induction significantly increased expression of other VSP-II encoded genes relative to the empty vector control Conclusions: our study represents the first analysis of a transcriptional regulator encoded on the VSP-II island

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30088

9 Samples

Download data: TXT, XLSX

(Submitter supplied) Zur is a transcription factor that represses zinc starvation response genes under zinc-rich conditions. Our goal was to identify candidate Zur-regulated genes by looking for transcripts significantly upregulated in the absence of Zur.

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30088

6 Samples

Download data: CSV, TXT

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

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL34020 GPL28681 GPL31913

76 Samples

Download data: BEDGRAPH, H5, TSV

(Submitter supplied) Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in different environments. more...

Organism:

Vibrio cholerae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34020

19 Samples

Download data: H5, R, TSV

(Submitter supplied) Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in different environments. more...

Organism:

Vibrio cholerae

Type:

Other

Platforms:

GPL31913 GPL28681 GPL34020

57 Samples

Download data: BEDGRAPH, NARROWPEAK

(Submitter supplied) Using a combination of ChIP-seq and RNA-seq we show that ToxT regulates expression of the small RNA TarB. TarB modulates the expression level of the transcriptioanl repressor VC0177. VC0177 controls expression of several genes including VC0179.

Organism:

Vibrio cholerae O1 str. C6706

Type:

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

Platforms:

GPL15333 GPL15332

23 Samples

Download data: TXT

(Submitter supplied) Burkholderia cepacia complex bacteria comprise opportunistic pathogens causing chronic respiratory infections in cystic fibrosis (CF) patients. These microorganisms produce exopolysaccharides which are considered virulence determinants. Here, we report the isolation of an evolved nonmucoid variant (17616nmv) after the ancestor, Burkholderia multivorans ATCC 17616, was subjected to prolonged stationary phase. more...

Organism:

Burkholderia multivorans; Burkholderia cenocepacia J2315; Burkholderia multivorans ATCC 17616

Type:

Expression profiling by array

Platform:

GPL13356

6 Samples

Download data: CEL

(Submitter supplied) Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of wild type (DB110) and toxR (TW30) mutant strains of the deep-sea bacterium Photobacterium profundum. ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae and able to regulate numerous genes involved in virulence. In P. profundum the abundance and activity of the same protein is influenced by hydrostatic pressure and is able to regulate genes in a pressure-dependent manner. more...

Organism:

Photobacterium profundum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15618

4 Samples

Download data: TXT

(Submitter supplied) H-NS family proteins are known as a member of nucleoid associated proteins (NAPs) conserved in genus Pseudomonas bacteria. Incompatibility group (Inc) P-7 archetype plasmid pCAR1 is transmissible among various Pseudomonas strains and carries genes encoding H-NS family protein, Pmr. P. putida KT2440 is one of pCAR1 hosts, which possesses five genes encoding H-NS family proteins, PP_1366 (TurA), PP_3765 (TurB), PP_0017 (TurC), PP_3693 (TurD), and PP_2947 (TurE) on its chromosome. more...

Organism:

Pseudomonas putida KT2440; Pseudomonas; Pseudomonas putida

Type:

Genome binding/occupancy profiling by genome tiling array; Expression profiling by genome tiling array

Platforms:

GPL8296 GPL6591

6 Samples

Download data: BAR, BED, CEL

(Submitter supplied) Histone-like nucleoid structuring (H-NS) and H-NS-like proteins serve as global gene silencers and work with antagonistic transcriptional activators (counter- silencers) to properly coordinate the expression of virulence genes in pathogenic bacteria. In Brucella, MucR has been proposed as a novel H-NS-like gene silencer, but direct experimental evidence is lacking. Here, we show that MucR serves as an H-NS-like silencer of the Brucella abortus genes encoding the polar autotransporter adhesins BtaE and BmaC, the c-di-GMP-specific phosphodiesterase BpdB, and the quorum-sensing regulator BabR. more...

Organism:

Brucella abortus 2308

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL33491

12 Samples

Download data: CSV, TXT