GEO DataSets

(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

(Submitter supplied) We performed a high-throughput systematic evolution of ligands by exponential enrichment (HT-SELEX) approach on all 371 annotated TFs in P. aeruginosa. This study provides a valuable resource for TF binding specificities in P. aeruginosa and demonstrates a novel and an integrative analysis for seeking the virulence-associated TFs and its target genes.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL28604 GPL28605

940 Samples

Download data: TXT

(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) Pseudomonas aeruginosa is one of the most common pathogens in hospital-acquired infection, which is tightly controlled by a multi-layered regulatory network including quorum sensing system (QS), type VI secretion system (T6SS) and resistance to host immunity. In the present study, we found that a PA3880 gene, which encodes an unknown protein, acted as a regulator of anaerobic metabolism, response to oxidative stress and virulence in P. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19430

8 Samples

Download data: XLSX

(Submitter supplied) We use high-throughput sequencing to profile the response of the opportunistic mucosal pathogen Pseudomonas aeruginosa to mucins and mucin-glycans from the mucosal niche. We find that P. aeruginosa undergoes a genome-wide phenotypic shift in response to mucins and their attached glycans. Specifically, nearly all virulence pathways are downregulated in response to these host-produced factors. This study provides a framework for understanding how the host environment regulates bacterial function.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

14 Samples

Download data: CSV

(Submitter supplied) Pseudomonas aeruginosa strains PAHM4 and PAO1 were grown at 37C on LB and RNA was hybridized on the Affymetrix P. aeruginosa chip to compare transcript differences from a BQ isolate to a well characterized wound isolate.

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1; Pseudomonas aeruginosa PAHM4

Type:

Expression profiling by array

Platform:

GPL84

6 Samples

Download data: CEL

(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) Characterization of bacterial behavior in the microgravity environment of spaceflight is of importance towards risk assessment and prevention of infectious disease during long-term missions. Further, this research field unveils new insights into connections between low fluid-shear regions encountered by pathogens during their natural infection process in vivo, and bacterial virulence. This study is the first to characterize the global transcriptomic and proteomic response of an opportunistic pathogen that is actually found in the space habitat, Pseudomonas aeruginosa. more...

Organism:

Pseudomonas aeruginosa PAO1; Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

8 Samples

Download data: CEL

(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) Gene expression profiles of two Pseudomonas aeruginosa taxonomic outlier clinical isolates, CLJ1 and CLJ3 [CLJ3] Pseudomonas aeruginosa taxonomic outliers emerged recently as infectious for humans, provoking hemorrhagic pneumonia. Those bacteria lack classical type III secretion system, and utilize the pore-forming toxin for infection. Two clones CLJ1 and CLJ3 belonging to these taxonomic outliers have been isolated from the same patient at two different times during hospitalization. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

2 Samples

Download data: TXT

(Submitter supplied) Gene expression profiles of two Pseudomonas aeruginosa taxonomic outlier clinical isolates, CLJ1 and CLJ3 [CLJ1] Pseudomonas aeruginosa taxonomic outliers emerged recently as infectious for humans, provoking hemorrhagic pneumonia. Those bacteria lack classical type III secretion system, and utilize the pore-forming toxin for infection. Two clones CLJ1 and CLJ3 belonging to these taxonomic outliers have been isolated from the same patient at two different times during hospitalization. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

2 Samples

Download data: TXT

(Submitter supplied) Pseudomonas aeruginosa is a significant opportunistic pathogen responsible for numerous human infections. Its high pathogenicity resides in a diverse array of virulence factors and an ability to adapt to hostile environments. We report that these factors are tied to the activity of condensins, SMC and MksBEF, which primarily function in structural chromosome maintenance. This study revealed that both proteins are required for P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20881

8 Samples

Download data: CSV, XLS

(Submitter supplied) Determination of the binding sites of 55 transcription factors (all response regulators) in Pseudomonas aeruginosa strains PAO1, PA14 and IHMA87.

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21297

342 Samples

Download data: XLSX

(Submitter supplied) Pseudomonas aeruginosa, a human opportunistic pathogen, is a common cause of nosocomial infections. Its ability to survive under different conditions relies on a complex regulatory network engaging transcriptional regulators controlling metabolic pathways and capabilities to efficiently use the available resources. P. aeruginosa PA3973 encodes a putative TetR family transcriptional regulator, with a helix-turn-helix motif involved in DNA binding. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21297 GPL26913

12 Samples

Download data: CSV, XLSX

(Submitter supplied) Pseudomonas aeruginosa PA3973 encodes a putative TetR family transcriptional regulator, with a helix-turn-helix motif involved in DNA binding. We applied phenotype analyses, as well as transcriptome profiling (RNA-seq), and genome-wide identification of binding sites using ChIP-seq to unravel the biological role of PA3973. The ChIP-seq analysis identified more than 300 PA3973 binding sites in the P. more...

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26913

4 Samples

Download data: BED, BIGWIG, FA

(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) Pseudomonas aeruginosa is a facultative human pathogen especially dangerous for immunocompromised patients. It is known from its high adaptability and complex regulatory systems involving huge repertoire of transcriptional regulators (TRs). The Lrp/AsnC family consists of proteins engaged mostly in regulation of processes such as amino acid metabolism but the function of most of them remains unknown. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21297

6 Samples

Download data: CSV

(Submitter supplied) Pseudomonas aeruginosa is a facultative human pathogen especially dangerous for immunocompromised patients. It is known from its high adaptability and complex regulatory systems involving huge repertoire of transcriptional regulators (TRs). The Lrp/AsnC family consists of proteins engaged mostly in regulation of processes such as amino acid metabolism but the function of most of them remains unknown. more...

Organism:

Pseudomonas aeruginosa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20881

3 Samples

Download data: BED, BIGWIG, FA

(Submitter supplied) Here, we report a CRISPR/Cas12k-transposon-assisted genome engineering (CTAGE) method that allows for high-throughput site-specific mutagenesis in microbial genomes. Exploiting the powerful CTAGE technique, we construct a site-specific transposon mutant library focusing on all the possible transcription factors (TFs) in Pseudomonas aeruginosa, enabling comprehensive identification of essential genes and new factors for antibiotic resistance.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Other

Platform:

GPL28604

10 Samples

Download data: TXT