GEO DataSets

(Submitter supplied) We developed an unbiased strategy for MOA prediction, called Perturbation-Specific Transcriptional Mapping (PerSpecTM), in which large-throughput expression profiling of wildtype or hypomorphic mutants, depleted for essential targets, enables a computational strategy to address this challenge. We applied PerSpecTM to perform reference-based MOA prediction based on the principle that similar perturbations, whether small molecule or genetic, will elicit similar transcriptional responses. more...

Organism:

Pseudomonas aeruginosa UCBPP-PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27892

1059 Samples

Download data: CSV

(Submitter supplied) The goal of this experiment was to determine the changes in the transcriptome of Pseudomonas aeruginosa when cultured in bronchoalveolar lavage fluid (BALF) from mice with oxygen-induced lung injury relative to healthy controls.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34956

18 Samples

Download data: TAR

(Submitter supplied) In nature, organisms experience combinations of stressors. However, laboratory studies use batch cultures, which simplify reality and focus on population-level responses to individual stressors. In recent years, bacterial stress responses have been examined with single-cell resolution using microfluidics. Here, we use a microfluidic approach to simultaneously provide a physical stressor (shear flow) and a chemical stressor (H2O2) to the human pathogen Pseudomonas aeruginosa. more...

Organism:

Pseudomonas aeruginosa PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28328

4 Samples

Download data: TXT

(Submitter supplied) C-di-GMP signaling can directly influence bacterial behavior by affecting the functionality of c-di-GMP-binding proteins. In addition, c-di-GMP can exert an indirect and more global effect on gene transcription or translation, e.g. via riboswitches or by binding to transcription factors. In this study, we investigated the effects of changes in intracellular c-di-GMP levels on gene expression and protein production in the opportunistic pathogen Pseudomonas aeruginosa. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28916 GPL18782

20 Samples

Download data: CSV, TXT

(Submitter supplied) In this study we compare logarithmically grown Pseudomonas aeruginosa wildtype to a transposon mutant that is disrupted in gshA, which is involved in glutathione biosynthesis using RNASeq to identify novel pathways where glutathione may be involved.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24583

6 Samples

Download data: TXT, XLSX

(Submitter supplied) The role of the intracellular signaling molecule diadenosine tetraphosphate (Ap4A) has not so far been investigated in Pseudomonas aeruginosa. To fill this gap, we performed RNA sequencing (RNA-seq) analysis to compare the transcriptome of the reference strain P. aeruginosa PAO1 and an isogenic deletion mutant (ΔapaH) which is deficient in the Ap4A hydrolysing enzyme ApaH and accumulates high intracellular levels of Ap4A.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

6 Samples

Download data: TXT

(Submitter supplied) Detecting chemical signals is important for identifying food sources and avoiding harmful agents. Like many animals, C. elegans use olfaction to chemotax towards their main food source, bacteria. However, little is known about the bacterial compounds governing C. elegans attraction to bacteria and the physiological importance of these compounds to bacteria. Here, we address these questions by investigating the function of a small RNA, P11, in the pathogen, Pseudomonas aeruginosa, that was previously shown to mediate learned pathogen avoidance. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

9 Samples

Download data: XLSX

(Submitter supplied) We aimed to illuminate the effects on the transcriptome upon translation knockdown (KD) of core genes and other characterised genes or early expressed genes in PHIKZ through anti-sense-based technology. We identified phage transcripts that are affected in level upon KD and clustering allowed to group these together that likely are expressed at a similar stage and dependency in the phage replication cycle. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34599

126 Samples

Download data: CSV, FASTA, GFF3, WIG

(Submitter supplied) ChmA forms the phage nucleus in PhiKZ-infected PAO1 cells, we aimed to illuminate the effects on the transcriptome upon knockdown (KD) of ChmA translation through anti-sense-based technology. We identified phage transcripts that are affected in level upon KD of ChmA and clustering allowed to group these together that likely are expressed at a similar stage and dependency in the phage replication cycle.

Organism:

Pseudomonas aeruginosa; Pseudomonas phage phiKZ

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34574

20 Samples

Download data: CSV, FA, GFF3, WIG

(Submitter supplied) Clinical case studies have reported that the combined use of specific lytic phage(s) and antibiotics reduces the severity of difficult-to-treat Pseudomonas aeruginosa infections in many patients. In vitro methods that attempt to reproduce specific pathophysiological conditions can provide a reliable assessment of the antibacterial effects of phages. Here, we measured bacterial killing kinetics and individual phage replication in different growth phases, including biofilms, elucidating factors influencing the efficacy of two phages against the laboratory strain P. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34679

12 Samples

Download data: XLSX

(Submitter supplied) PsrA, a transcription factor belonging to the TetR family, is known to participate in the regulation of fatty acid metabolism, type III secretion system, and quinolone signaling in Pseudomonas aeruginosa. Using a psrA overexpression strain, this study conducted a transcriptomic analysis to examine the role of PsrA in P. aeruginosa PAO1.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24583

2 Samples

Download data: XLSX

(Submitter supplied) To determine whether flow alters the gene expression of planktonic P. aeruginosa, we designed a long microfluidic channel that enabled us to expose bacteria to flow for significant lengths of time and then be fixed as they exit the channel. The experiments mimic the kinds of shear flows characteristic of a wide variety of confined flow configurations. Using this microfluidic system, we performed bulk RNA-Seq analysis of planktonic bacteria that flowed for 55 min at a shear rate of 20 per second, and compared gene expression of this population with a control population of planktonic bacteria under similar conditions with no flow.

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34599 GPL34676

6 Samples

Download data: TXT

(Submitter supplied) Pyruvate dehydrogenase (PDH) catalyses the irreversible decarboxylation of pyruvate to acetyl-CoA, which feeds the tricarboxylic acids cycle. We analysed how the lack of PDH affects Pseudomonas putida metabolism. Inactivating PDH generated a strain that can no longer use compounds whose assimilation converges into pyruvate, including sugars and several amino acids. Compounds generating acetyl-CoA supported growth. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18287

6 Samples

Download data: TXT

(Submitter supplied) It is becoming increasingly apparent that commensal skin bacteria have an important role in wound healing and infection progression. However, the precise mechanisms underpinning many of these probiotic interactions remain to be fully uncovered. In this work, we demonstrate that the common skin commensal Cutibacterium acnes can limit the pathogenicity of the prevalent wound pathogen Pseudomonas aeruginosa in vivo. more...

Organism:

Pseudomonas aeruginosa PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33546

6 Samples

Download data: TSV

(Submitter supplied) RNA helicases—central enzymes in RNA metabolism— often feature intrinsically disordered regions (IDRs) that enable phase separation and complex interactions with other proteins and/or RNA molecules. IDRs are varied and fast evolving, which makes their function hard to predict. In the bacterial pathogen Pseudomonas aeruginosa, two non-redundant RNA helicases, RhlE1 and RhlE2, share a conserved REC catalytic core but have different C-terminal extensions (CTEs) composed of IDRs of diverse length and amino acid composition. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

36 Samples

Download data: XLSX

(Submitter supplied) Pseudomonas aeruginosa (PA) is an opportunistic pathogen frequently isolated from cutaneous chronic wounds. How PA, in the presence of oxidative stress (OS), colonizes chronic wounds and forms a biofilm is still unknown. The purpose of this study is to investigate the changes in gene expression seen when PA is challenged with the high levels of OS present in chronic wounds. We used a biofilm-forming PA strain isolated from the chronic wounds of our murine model (RPA) and performed a qPCR to obtain gene expression patterns as RPA developed a biofilm in vitro in the presence of high levels of OS, and then compared the findings in vivo, in our mouse model of chronic wounds. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

18 Samples

Download data: TXT

(Submitter supplied) Purpose: The purpose of this study was to investigate the effect of quorum sensing on phage infection. Methods: We constructed the lasR gene knockout strain of Pseudomonas aeruginosa PAO1 and performed transcriptome sequencing.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

6 Samples

Download data: TSV, TXT

(Submitter supplied) Methylrhodomelol (1) is a bromophenol from the red alga Vertebrata lanosa (L.) T.A.Christensen that has been associated with antimicrobial properties. Aim of the current study was therefore, to assess the antimicrobial potential of this compound in more detail against the gram-negative pathogen Pseudomonas aeruginosa. 1 exerted weak bacteriostatic activity against different strains when grown in minimal medium, whereas other phenolics were inactive. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33271

6 Samples

Download data: TXT

(Submitter supplied) RNA modifications have a substantial impact on tRNA function. While modifications in the anticodon loop play an important role in translational fidelity, modifications in the tRNA core influence tRNA structural stability. In bacteria, tRNA modifications play important roles in the stress response and expression of virulence factors. While tRNA modifications are well characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa is lacking. more...

Organism:

Pseudomonas aeruginosa PA14; Escherichia coli BW25113

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL25344 GPL33546 GPL30881

27 Samples

Download data: CSV, FA, TXT

(Submitter supplied) Efflux pumps of the resistance-nodulation-division (RND) superfamily, particularly the AcrAB-TolC and MexAB-OprM, besides mediating intrinsic and acquired resistance, also intervene in bacterial pathogenicity. Inhibitors of such pumps could restore activities of antibiotics and curb bacterial virulence. Here, we identify pyrrole-based compounds that boost antibiotic activity in Escherichia coli and Pseudomonas aeruginosa by inhibiting their archetype RND transporters. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26913

6 Samples

Download data: XLSX