GEO DataSets

(Submitter supplied) In this study we determined the gene expression of the whole genome of V. cholerae during the interaction with THP-1 derived macrophages by RNA-sequencing.

Organism:

Homo sapiens; Vibrio cholerae O1 biovar El Tor

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30626 GPL30627

36 Samples

Download data: CSV, GTF, TXT, XLSX

(Submitter supplied) In this study we determined the gene expression of THP-1 derived macrophages during the interaction with V. cholerae wildtype cells, biofilm-deficient or hemolysin-deficient mutants.

Organism:

Homo sapiens; Vibrio cholerae O1 biovar El Tor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30626

1 Sample

Download data: CSV, TXT, XLS, XLSX

(Submitter supplied) This study was conducted to study which genes or functions become important or expendable in two V. cholerae mutants compared to the WT. This was assessed directly by conjugating a Mariner Transposon with WT or mutant cells and obtaining a bank of hundreds of thousands of mutants which we consider as the T=0. We then subjected these banks to 16 generations in rich media with or without 50% MIC of tobramycin (which we call T=16gen). more...

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Other

Platform:

GPL32053

27 Samples

Download data: XLSX

(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 WT and tgt mutant strains in MH medium in the presence or not of sublethal concentration on tobramycin or ciprofloxacin

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30088

18 Samples

Download data: XLSX

(Submitter supplied) We study gene expression levels of V. cholerae N16961 WT and crp mutant strains/V. cholerae N16961 hapR+ corrected strain, ravAviA mutant and ravAviA overexpressing strains in exponential phase in MH, MH+maltose 0.4% and MH+glucose 0.4%

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30088

45 Samples

Download data: TXT

(Submitter supplied) In this study, we show that ManR (VC1825) activates the transcription of the mannose operon in M9 medium supplemented with fructose or mannose, and when manR is impaired Vibrio cholerae cells fail to colonize the intestine and host survival is significantly prolonged in a fruit fly Drosophila melanogaster infection model. To identify other target genes of ManR, transcriptome analysis was performed in wild-type V. more...

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31160

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

(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) Bactericidal antibiotics are powerful drugs because they not only inhibit essential bacterial functions, but convert them into toxic processes. Many bacteria are remarkably tolerant against antibiotics, due to inducible damage repair responses. How these responses promote whole population tolerance in important human pathogens is poorly understood. The two-component system VxrAB of the diarrheal pathogen Vibrio cholerae, a model system for tolerance against cell wall damaging (e.g., beta-lactam) antibiotics, is required for high-level beta-lactam tolerance. more...

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26987

6 Samples

Download data: GFF, XLSX

(Submitter supplied) Bactericidal antibiotics are powerful drugs because they not only inhibit essential bacterial functions, but convert them into toxic processes. Many bacteria are remarkably tolerant against antibiotics, due to inducible damage repair responses. How these responses promote whole population tolerance in important human pathogens is poorly understood. The two-component system VxrAB of the diarrheal pathogen Vibrio cholerae, a model system for tolerance against cell wall damaging (e.g., beta-lactam) antibiotics, is required for high-level beta-lactam tolerance. more...

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26987

8 Samples

Download data: GFF, XLSX

(Submitter supplied) Blue light (BL) is a major environmental factor that affects the physiology, behavior, and infectivity of bacteria as it contributes to the generation of reactive oxygen species (ROS) while increasing photo-oxidative stress in cells. However, precise photo-oxidative response mechanism in non-phototrophic bacteria is yet to be elucidated. In this study, we investigated the effect of BL in Vibrio cholerae by using genetics and transcriptome profiling. more...

Organism:

Vibrio cholerae O1 biovar El Tor str. N16961

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21692

14 Samples

Download data: XLSX

(Submitter supplied) Heritable DNA methylation imprints occur in most genomes and underlie genetic variability in humans. The mechanism and consequences of establishing and propagating local hypomethylation through consecutive rounds of DNA replication and intermittent cell division cycles are poorly understood. Our genome-wide and site-specific methyl-N6-adenine (m6A-) analyses reveal a conserved local hypomethylation mechanism in two α-proteobacterial model systems. more...

Organism:

Vibrio cholerae O1 biovar El Tor; Caulobacter vibrioides NA1000; Escherichia coli str. K-12 substr. MG1655; Caulobacter vibrioides; Sinorhizobium meliloti

Type:

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

7 related Platforms

16 Samples

Download data: CSV, GFF, 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) 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) Replication and segregation are the two main processes that maintain chromosomes in growing cells. In bacteria, replication and transcription have been proposed to provide motive force in chromosome segregation. Recently, ParB2, a segregation protein, encoded by V. cholerae chromosome II (chrII) was also found to influence chrII replication. V. cholerae chrII replication is primarily controlled by its specific initiator protein, RctB. more...

Organism:

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

Type:

Genome binding/occupancy profiling by array

Platform:

GPL20909

8 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling comparing a V. cholerae cpxA* mutant relative to WT at an OD600 of 1.

Organism:

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

Type:

Expression profiling by array

Platform:

GPL3651

6 Samples

Download data: GPR