txid286[Organism] - GEO DataSets

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Select item 2002612421.

mgo promotes the expression of a gene cluster that contributes to the survival of Pseudomonas syringae in tomato leaflets

(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

Series

Accession:: GSE261242

ID:: 200261242

Select item 2002516712.

Perturbation-Specific Transcriptional Mapping for unbiased target elucidation of antibiotics

(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

Series

Accession:: GSE251671

ID:: 200251671

Select item 2002785423.

Determining the Injury-Associated Microbial Nutrients that Facilitate Secondary Bacterial Infection in Acutely Injured Lungs

(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

Series

Accession:: GSE278542

ID:: 200278542

Select item 2002775314.

Environmental alkalization suppresses deployment of virulence strategies in Pseudomonas syringae pv. tomato DC3000

(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

Series

Accession:: GSE277531

ID:: 200277531

Select item 2002778115.

Combining multiple stressors unexpectedly blocks bacterial migration and growth

(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

Series

Accession:: GSE277811

ID:: 200277811

Select item 2002665906.

Gene expression of P. putida KT2440 cultivated in an anoxic bioelectrochemical system

(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

Series

Accession:: GSE266590

ID:: 200266590

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001833947.

Pseudomonas aeruginosa post-translational responses to elevated c-di-GMP levels

(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

Series

Accession:: GSE183394

ID:: 200183394

SRA Run Selector

Select item 2002408288.

Transcriptional analysis of transposon mutants disrupted in glutathione biosynthesis in Pseudomonas aeruginosa

(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

Series

Accession:: GSE240828

ID:: 200240828

Select item 2002558639.

The diadenosine tetraphosphate hydrolase ApaH is crucial for Pseudomonas aeruginosa pathogenicity

(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

Series

Accession:: GSE255863

ID:: 200255863

PubMed Full text in PMC Similar studies

Select item 20027375110.

Pseudomonas aeruginosa controls both Caenorhabdtitis elegans attraction and pathogenesis by regulating nitrogen assimilation

(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

Series

Accession:: GSE273751

ID:: 200273751

Select item 20026991111.

RNA-seq after knockdown of PhiKZ genes in PhiKZ-infected Pseudomonas aeruginosa PAO1 cells

(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

Series

Accession:: GSE269911

ID:: 200269911

Select item 20026940112.

RNA-seq after chmA knockdown in PhiKZ-infected PAO1 cells

(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

Series

Accession:: GSE269401

ID:: 200269401

Select item 20027153713.

Interphage competition and biofilms reduce the lytic effect of two phages against Pseudomonas aeruginosa

(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

Series

Accession:: GSE271537

ID:: 200271537

Select item 20024951814.

Comparative transcriptomic profiling of overexpression of PsrA in Pseudomonas aeruginosa PAO1

(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

Series

Accession:: GSE249518

ID:: 200249518

PubMed Full text in PMC Similar studies

Select item 20027142615.

RNA-Seq of Planktonic P. aeruginosa in flow

(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

Series

Accession:: GSE271426

ID:: 200271426

PubMed

Select item 20026320816.

Inactivation of Pseudomonas putida KT2440 pyruvate dehydrogenase relieves catabolite repression and improves the usefulness of this strain as a tool in biotechnology

(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

Series

Accession:: GSE263208

ID:: 200263208

PubMed Full text in PMC Similar studies

Select item 20023640517.

Carbon source competition within a wound can significantly influence infection progression.

(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

Series

Accession:: GSE236405

ID:: 200236405

PubMed Full text in PMC Similar studies

Select item 20021615718.

Hfq mediates transcriptome-wide RNA structurome reprogramming under virulence-inducing conditions in a phytopathogen

(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

Series

Accession:: GSE216157

ID:: 200216157

PubMed Similar studies

Select item 20026999219.

Complete Genome Sequencing and Transcriptome Analysis of aniline-degrading strain T1

(Submitter supplied) The aniline-degrading strain T1 can efficiently degrade aniline, however, it is not clear which key genes are associated with aniline degradation, and we have adopted a genome-wide and transcriptomic approach to fully understand the microbial degradation mechanism of aniline.

Organism:: Pseudomonas veronii

Type:: Expression profiling by high throughput sequencing

Platform:: GPL34605
6 Samples

Download data: TXT

Series

Accession:: GSE269992

ID:: 200269992

Select item 20024739520.

Architecture of the genome-wide transcriptional regulatory network reveals the dynamic biological functions and divergent evolutionary trajectory in Pseudomonas syringae

(Submitter supplied) The model Gram-negative plant pathogen Pseudomonas syringae utilizes hundreds of transcription factors (TFs) to manipulate its functional processes, including virulence and metabolic pathways to control its infection to host plants. Although the molecular mechanisms of regulators have been studied for decades, the comprehensive understanding throughout the genome-wide TFs in P. syringae remains uncertain. more...

Organism:: Pseudomonas syringae pv. actinidiae str. Shaanxi_M228; Pseudomonas syringae pv. syringae B728a; Pseudomonas syringae pv. tomato str. DC3000; Pseudomonas savastanoi pv. phaseolicola 1448A

Type:: Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms
396 Samples

Download data

Series

Accession:: GSE247395

ID:: 200247395

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