GEO DataSets

(Submitter supplied) The Pseudomonas aeruginosa quorum-sensing (QS) systems contribute to bacterial homeostasis and pathogenicity. Although many regulators have been characterized to control the production of virulence factors and QS signaling molecules, its detailed regulatory mechanisms still remain elusive. Here, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) on 10 key QS regulators. more...

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18644

20 Samples

Download data: TXT

(Submitter supplied) The Pseudomonas aeruginosa response regulator AlgR is critical for the organism's virulence and controls up to 155 different genes. In order to determine which genes are controlled by phosphorylated and unphosphorylated AlgR, phosphomimetic and phosphoablative alleles were recombined onto the chromosome of PAO1. The algR gene was mutated at aspartate 54 to asparagine (D54N) for the phosphoablative allele and mutated at aspartete 54 to glutamate (D54E) for the phosphomimetic allele. more...

Organism:

Pseudomonas aeruginosa PAO1; Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

9 Samples

Download data: CEL, CHP

(Submitter supplied) Microarray analysis for the biofilm cells of Pseudomonas aeruginosa PA14 wild-type vs the tpbA (PA14_13660) mutant in LB medium at 4 and 7 h at 37C

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

6 Samples

Download data: CEL

(Submitter supplied) The c-di-GMP regulon in C. difficile

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22510

8 Samples

Download data: XLSX

(Submitter supplied) We analyzed a deletion mutant of the ECF σ factor SigX and applied mRNA profiling to define the SigX dependent regulon in P. aeruginosa in response to low osmolarity medium conditions. Furthermore, the combination of transcriptional data with chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing led to the identification of the DNA binding motif of SigX. Genome-wide mapping of SigX-binding regions revealed enrichment of downstream genes involved in fatty acid biosynthesis, type III secretion, swarming and c-di-GMP signaling. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

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

Platforms:

GPL17739 GPL17738

12 Samples

Download data: TXT

(Submitter supplied) The cholera disease bacterium V. cholerae, can adopt planktonic or biofilm lifestyles depending on the intracellular concentration of the second messenger cyclic diguanylic acid (c-di-GMP). Biofilm formation protects Vibrios from stressful conditions and facilitates disease transmission by enhancing infectivity. The histone-like nucleoid structuring protein (H-NS) is a global regulator of genes associated with pathogenicity and responses to environmental stresses. more...

Organism:

Vibrio cholerae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19265

2 Samples

Download data: BED, WIG, XLS

(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) The Pseudomonas aeruginosa quorum-sensing (QS) systems contribute to bacterial homeostasis and pathogenicity. Although the AraC family transcription factor VqsM has been characterized to control the production of virulence factors and QS signaling molecules, its detailed regulatory mechanisms still remain elusive. Here, we report that VqsM directly binds to the lasI promoter region, and thus regulates its expression. more...

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18644

4 Samples

Download data: TXT

(Submitter supplied) Although the ubiquitous bacterial secondary messenger cyclic diguanylate (c-di-GMP) plays important roles in various cellular functions including the formation of biofilm in a wide range of bacteria, its function in model plant pathogen Pseudomonas syringae is largely elusive. In order to test this in P. syringae, we overexpressed a diguanylate cyclase (YedQ) and a phosphodiesterase (YhjH) that are originally from Escherichia coli, resulting in high and low c-di-GMP levels in P. more...

Organism:

Pseudomonas syringae pv. syringae B728a

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25646

6 Samples

Download data: XLSX

(Submitter supplied) In this study, we used transcriptional profiling to define the adaptive response of C. violaceum to oxidative stress induced by cumene hydroperoxide (CHP) and to identify the OhrR regulon. DNA microarray and northern blot analysis revealed that in CHP-treated cells occur strong upregulation of genes involved in many pathways for stress protection, including antioxidant enzymes (catalase and peroxidases), thioredoxin, glutaredoxin and lipoyl-dependent reducing systems, DNA repair enzymes, heat shock response (σ32 regulon), iron limitation (Fur regulon) and nitrogen starvation. more...

Organism:

Chromobacterium violaceum; Chromobacterium violaceum ATCC 12472

Type:

Expression profiling by array

Platform:

GPL22705

6 Samples

Download data: TXT

(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) In Myxococcus xanthus 55% of the more than 250 two-component signal transduction systems (TCS) genes are orphan. We hypothesized that the histidine kinase SgmT and the response regulator DigR, which comprises a DNA binding domain of the HTH_Xer type, function together to regulate gene expression. We performed genome-wide expression profiling experiments to determine wether the same set of genes are differentially expressed in the ΔdigR and ΔsgmT mutants.

Organism:

Myxococcus xanthus

Type:

Expression profiling by array

Platform:

GPL8535

6 Samples

Download data: GPR

(Submitter supplied) Pseudomonads typically carry multiple non-identical alleles of the post-transcriptional regulator rsmA. In P. aeruginosa, RsmN is notable in that its structural rearrangement confers distinct and overlapping functions with RsmA. However, little is known about the specificities RsmN for its target RNAs and overall impact on the biology of this pathogen. We purified and mapped 503 transcripts directly bound by RsmN in P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20881

10 Samples

Download data: TXT, WIG

(Submitter supplied) Pseudomonas aeruginosa encodes a large set of transcriptional regulators which allow to modulate and manage cellular metabolism to survive in variable environmental conditions, including the human body. The AraC family regulators are an abundant group of transcriptional regulators in bacteria, mostly acting as gene expression activators controlling diverse cellular functions e.g. carbon metabolism, stress response and virulence. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20881

6 Samples

Download data: CSV

(Submitter supplied) Pseudomonas aeruginosa encodes a large set of transcriptional regulators which allow to modulate and manage cellular metabolism to survive in variable environmental conditions, including the human body. The AraC family regulators are an abundant group of transcriptional regulators in bacteria, mostly acting as gene expression activators controlling diverse cellular functions e.g. carbon metabolism, stress response and virulence. more...

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20881

5 Samples

Download data: BIGWIG

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

Organism:

Pseudomonas aeruginosa

Type:

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

Platforms:

GPL20881 GPL26913 GPL21297

55 Samples

Download data: BIGWIG

(Submitter supplied) Vibrio parahaemolyticus scr genes modulate expression of gene sets pertinent to swarming and biofilm formation. They do so by affecting the level of the second messenger c-di-GMP. Here we explore the extent of this regulation by comparing the transcriptomes of a scrABC mutant and its wild-type parental strain. The scope of transcriptional effects modulated by c-di-GMP includes ~100 genes that are positively and negatively regulated. more...

Organism:

Vibrio parahaemolyticus; Vibrio parahaemolyticus RIMD 2210633

Type:

Expression profiling by array

Platform:

GPL8837

4 Samples

Download data: CEL, TXT

(Submitter supplied) The PA0336 protein from Pseudomonas aeruginosa belongs to the family of widely distributed Nudix pyrophosphohydrolases which catalyze the hydrolysis of pyrophosphate bonds in a variety of nucleoside diphosphate derivatives. The amino acid sequence of the PA0336 protein is highly similar to that of the RppH Nudix RNA pyrophosphohydrolase from E. coli which removes pyrophosphate from 5’-end of triphosphorylated RNA transcripts. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23385

6 Samples

Download data: TXT

(Submitter supplied) Regulatory networks including virulence-related transcriptional factors (TFs) determine bacterial pathogenicity in response to different environmental cues. Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen of humans, recruits numerous TFs in quorum sensing (QS) system, type III secretion system (T3SS) and Type VI secretion system (T6SS) to mediate the pathogenicity. Although many virulence-related TFs have been illustrated individually, very little is known about their crosstalks and regulatory network. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

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

Platform:

GPL19430

52 Samples

Download data: TXT, XLSX

(Submitter supplied) Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen of humans, most notably those with cystic fibrosis or whose immune systems are compromised. As a global regulator, MvfR,RhlR and QscR have been characterized to control a group of virulence-related factors and quorum sensing (QS) genes in P. aeruginosa, but its detailed molecular regulatory mechanism is largely elusive. To further gain insights into the direct targets of MvfR,RhlR and QscR in viv, this study focused on identifying the potential targets of MvfR,RhlR and QscR directly regulating QS system and other vireulence pathways. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19430

10 Samples

Download data: XLSX