GEO DataSets

(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) We show that ZS1 in the medium supplemented with YE (YE-medium) produces more cell biomass but less rhamnolipid than it does in Glc-medium. To elucidate the transcriptional regulation of genes that are involved in biosynthesis of rhamnolipids and its precursors, RNA-seq-based transcriptional profiling of ZS1 cells in response to reciprocal change of YEand Glc-media is performed. Based on the assembly of ZS1 transcriptome using the reference PAO1 genome, we show that genes involved in energy metabolic pathways in ZS1 strain are highly transcribed in YE medium but not in Glc-medium, in agreement with their cell mass production. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

8 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAS71 (RNA-seq) to transcriptome profiling of LVX-treated P. aeruginosa PAS71 and to evaluate protocols for optimal high-throughput data analysis. Methods:LB medium (50 mL) was inoculated with exponential growth phase P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

6 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAS81 (RNA-seq) to transcriptome profiling of LVFX-treated P. aeruginosa PAS81 and to evaluate protocols for optimal high-throughput data analysis. Methods:LB medium (50 mL) was inoculated with exponential growth phase P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

6 Samples

Download data: TXT

(Submitter supplied) Multidrug (MDR) efflux pumps are ancient and conserved molecular machineries with relevant roles in different aspects of the bacterial physiology, besides antibiotic resistance. In the case of the environmental opportunistic pathogen Pseudomonas aeruginosa, it has been shown that overexpression of different efflux pumps is linked to the impairment of the quorum sensing (QS) response. Nevertheless, the causes of such impairment are different for each analyzed efflux pump. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

4 Samples

Download data: XLSX

(Submitter supplied) Analysis of Pseudomonas aeruginosa PAO1 (ATCC 15692) treated by Tanreqing. PAO1 cells are evaluated with RNA-seq to understand the genes affected by this antibacterial agent. Our results provide new vision on the mode of action by Tanreqing.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

12 Samples

Download data: TXT

(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) 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

15 Samples

Download data: CSV

(Submitter supplied) Purpose: Pseudomonas aeruginosa is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). We provide an insight to the DNA auxotrophy of P. aeruginosa PASS4 isolate. Better understanding of P. aeruginosa adaptations in the CF lung environment can have a great impact in the development of specialised treatment regimes aimed at the eradications of P. aeruginosa infections. Methods: P. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

12 Samples

Download data: TXT

(Submitter supplied) The purpose of this experiment was to see if the addition of sialic acid activated the GacS-GacA regulon, which includes >300 genes.

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 [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 known to tolerate antibiotic therapy during infection. This prevents clearance of infection and negatively impacts patient outcomes. Here, we report the transcriptome sequence of antibiotic-treated and untreated P. aeruginosa cultures and the differential gene expression observed when treated cells are compared to untreated cells.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

8 Samples

Download data: TXT

(Submitter supplied) We report the different bactericidal ability of endolysin wild type and mutant and explain the pathway of lipopolysaccharide biosynthesis is the dominant factor.

Organism:

Escherichia coli; Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18644 GPL14548

6 Samples

Download data: TXT

(Submitter supplied) RNAseq analysis was performed to evaluate gene expression differences between strains 1-9 and PAK-AR2.P. aeruginosa PAK-AR2 and 1-9 cells were grown to OD600 of 0.8 before harvesting. The collected cells were treated with RNAprotect Bacteria Reagent (Qiagen) and subjected to snap freezing in liquid nitrogen and delivered to BGI in dry ice for transcriptome resequencing analysis.The differentially expressed genes (DEGs) were determined between PAK-AR2 and 1-9 with the standards of false discovery rate (FDR ) ≤ 0.001, fold change |log2Ratio|≥1.A total of 4,355,305 reads matched to the referenced genome in the sample of PAK-AR2, and 3,544,484 reads in the sample of 1-9.Transcriptome data showed that expression of 361 genes were upregulated while 459 genes were down regulated by at least 2-fold when comparing the srpA mutant strain 1-9 to its parent strain PAK-AR2.These genes were classified into 21 major cellular processes based on the annotation of KEGG_B_class or further grouped into several major metabolic pathways, such as ribosomal proteins, type III secretion system (T3SS), type VI secretion system (T6SS), chemotaxis, cell motility, and cell shape control.More and more small proteins that were ignored from typical genome annotations have now been experimentally demonstrated to play important regulatory roles on various bacterial metabolic.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

2 Samples

Download data: TXT

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

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

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

Platforms:

GPL18644 GPL19430

24 Samples

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(Submitter supplied) Intrinsic and acquired defenses against bacteriophages, including Restriction/Modification, CRISPR/Cas, and Toxin/Anti-toxin systems have been intensely studied, with profound scientific impacts. However, adaptive defenses against phage infection analogous to adaptive resistance to antimicrobials have yet to be described. To identify such mechanisms, we applied an RNAseq-based, comparative transcriptomics approach in different \textit{Pseudomonas aeruginosa} strains after independent infection by a set of divergent virulent bacteriophages. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18644 GPL20881

29 Samples

Download data: XLSX

(Submitter supplied) Purpose: The intensive use of metal-based nanoparticles results in their continuous release into the environment and the subsequent destroying microbial biodiversity and causing occurrence of antibiotic resistant determinants. Although previous studies have indicated that nanoparticles may be toxic to microorganisms, there is a scarcity of data available to assess the underlying molecular mechanisms of inhibitory and biocidal effects of nanoparticles on microorganisms, which is a critical gap in our comprehensive understanding of the impacts of nanoparticles on microbial ecosystems. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

4 Samples

Download data: XLSX

(Submitter supplied) We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P4 infecting PAK strain of P. more...

Organism:

Pseudomonas aeruginosa; Pseudomonas phage PAK_P4

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18644 GPL22367

12 Samples

Download data: XLS, XLSX

(Submitter supplied) PA3225 is a LysR-type transcriptional regulator, and the ΔPA3225 deletion mutant is more resistant to various antibiotics than the wild-type PA14 strain in both planktonic and biofilm cells. In order to characterise the regulon of PA3225, we compared the transcriptomes of biofilm and planktonic ΔPA3225 to biofilm and planktonic PA14 wild-type by RNA-seq.

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18644

12 Samples

Download data: TSV