GEO DataSets

(Submitter supplied) In our previous work, we found that the root exudates of sgn3 myb36 promoted the colonization of CHA0 on roots. Through LC-MS, we identified a large amount of glutamine (Gln) in the root exudates of sgn3 myb36. Therefore, we aim to use RNA-seq to uncover whether the root exudates of sgn3 myb36 and Gln have the same regulatory effects on CHA0. By conducting differential analysis with the CK (CHA0 treated with wild-type root exudates), we hope to identify the specific regulatory mechanisms of sgn3 myb36 and Gln on CHA0.

Organism:

Pseudomonas protegens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35063

9 Samples

Download data: CSV

(Submitter supplied) RNA-seq analysis of Pseudomonas sp OST1909 exposed to various preparations of naphthenic acids samples led to the identiifcation of many NA-induced genes.

Organism:

Pseudomonas sp. OST1909

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34317

8 Samples

Download data: TSV

(Submitter supplied) Pseudomonas syringae is an important plant pathogen that infects a wide variety of crops. The mgo (mangotoxin-generating operon) gene cluster produces an extracellular signaling molecule, leudiazen, and is highly conserved in Pseudomonas syringae strains. Here, we genetically removed mgo in Pseudomonas syringae pv. syringae (Pss) UMAF0158 to interrogate its impacts on bacterial infection. Loss of mgo not only alleviated the chlorosis symptom caused by Pss UMAF0158 infection, but also reduced bacterial population in tomato leaflets. more...

Organism:

Pseudomonas syringae pv. syringae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34164

6 Samples

Download data: TXT

(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) Plant pathogenic bacteria encounter a drastic increase in apoplastic pH during the early stages of plant immunity. The effects of alkalization on pathogen-host interactions have not been comprehensively characterized. Here we used a global transcriptomic approach to assess the impact of environmental alkalization on Pseudomonas syringae pv. tomato DC3000 in vitro. In addition to the Type 3 Secretion System (T3SS), we found expression of genes encoding other virulence factors such as iron uptake, and coronatine biosynthesis to be strongly affected by environmental alkalization. more...

Organism:

Pseudomonas syringae pv. tomato str. DC3000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34917

18 Samples

Download data: TXT

(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) To get insights in the electrogenic anaerobic lifestyle of P. putida KT2440 cultivated in a bioelectrochemical system (BES), we employed whole genome microarray expression profile.

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by array

Platform:

GPL31933

12 Samples

Download data: TXT, XLSX

(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:

GPL18782 GPL28916

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:

GPL34676 GPL34599

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) Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. more...

Organism:

Pseudomonas savastanoi pv. phaseolicola 1448A

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24018

28 Samples

Download data: BED, TXT