Dkstatin-treated Pseudomonas aeruginosa trascriptome
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ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa
PROVIDER: GSE163248 | GEO | 2020/12/16
REPOSITORIES: GEO
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Project description:In order to understand how Pseudomonas aeruginosa responds to low oxygen we grew strain PAO1 with 3 different oxygen concentrations: 2%, 0.4% and 0% supplemented with nitrate as an electron acceptor. Gene expression under these conditions was compared to that of cells grown with 20% oxygen. Keywords: Comparison of transcriptome profiles
2007-05-17 | GSE6741 | GEO
Project description: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 PAO1 (RNA-seq) to transcriptome profiling of DAS-treated and DAE-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis. Results: The transcriptome sequencing data of control, DAS-treated and DAE-treated groups were compared and analyzed in the form of the following: DAE vs DAS, control vs DAS, and control vs DAE. The details of the differentially expressed genes among the three groups showed that the amount of differential expressed genes between DAE-treated group and DAS-treated group was high (total 2195, up-regulated 1608, down-regulated 587). There were many differentially expressed genes in the PAO1 strain after DAS treatment (total 2771, up-regulated 1905, down-regulated 866), while the amount of differentially expressed genes after DAE treatment was relatively small (total 770, up-regulated 349, down-regulated 421).
2020-12-31 | GSE151292 | GEO
Project description: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.
2020-11-19 | GSE141753 | GEO
Project description:Analysis of Pseudomonas aeruginosa PAO1 treated with 200 µM sphingomyelin. Results provide insight into the response to sphingomyelin in P. aeruginosa.
2017-02-12 | GSE83078 | GEO
Project description:Pseudomonas aeruginosa PAO1 contacted with and without poplar roots gene expression Poplar contacted with and without PAO1 gene expression. All samples cultured in 1 x hrp + 0.25 % sucrose Keywords: Contact with different species
2007-03-18 | GSE5887 | GEO
Project description:The ParS/ParR two component regulatory system plays important roles for multidrug resistance in Pseudomonas aeruginosa. In this study we report RNA-seq analyses of the transcriptomes of P. aeruginosa PAO1 wild type and par mutants growing in a minimal medium containing 2% casamino acids. This has allowed the quantification of PAO1 transcriptome, and further defines the regulon that is dependent on the ParS/ParR system for expression. Our RNA-seq analysis produced the first estimates of absolute transcript abundance for the 5570 coding genes in P. aeruginosa PAO1. Comparative transcriptomics of P. aeruginosa PAO1 and par mutants identified a total of 464 genes regulated by ParS and ParR. Results also showed that mutations in the parS/parR system abolished the expression of the mexEF-oprN operon by down-regulating the regulatory gene mexS. In addition to affecting drug resistance genes, transcripts of quorum sensing genes (rhlIR and pqsABCDE-phnAB), were significantly up-regulated in both parS and parR mutants. Consistent with these results, a significant portion of the ParS/ParR regulated genes belonged to the MexEF-OprN and quorum sensing regulons. Deletion of par genes also lead to overproduction of phenazines and increased swarming motility, consistent with the up-regulation of quorum sensing genes. Our results established a link among ParS/ParR, MexEF-OprN and quorum sensing in Pseudomonas aeruginosa. Based on these results, we propose a model to illustrate the relationship among these regulatory systems in P. aeruginosa.
2016-02-26 | GSE44681 | GEO
Project description: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 PAO1 (RNA-seq) to transcriptome profiling of farnesol-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis. Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 108 CFU/mL. Farnesol was then added at a concentration of either 0 (control) or 0.56 mg/mL, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three farnesol treatment groups, respectively. The cell precipitates were separately snap-frozen at -80ºC. Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol. Results: Our RNA-seq results showed that less than 100 genes of P. aeruginosa PAO1 were differentially expressed following farnesol treatment. We found that about 1.7% of all detected genes (96 of 5554 genes) were more than two-fold differentially expressed following farnesol treatment. Conclusions:
2019-10-11 | GSE138731 | GEO
Project description:Azithromycin-treated PAO1 vs untreated PAO1
| PRJNA91591 | ENA
Project description:As production of virulence factors by Pseudomonas aeruginosa is influenced by the host environment, we examined the effect of 10% adult bovine serum (ABS) on the global transcription with P. aeruginoas PAO1 at different phases of growth. At early exponential phase (4 h), serum significantly enhanced expression of 138 genes, most of which are repressed by iron and carry binding sequences for the ferric uptake regulator or the Fur-regulated extracytoplasmic function sigma factor PvdS. The expression of another 40 genes was reduced at 4h. However, the expression of only a few genes was significantly altered (reduced) at the early stationary phase of growth (8 h). Transcriptional fusion analyses confirmed serum enhances the expression of toxA, regA, and their regulatory genes regA and pvdS, yet does not interfere with the repression of these genes by iron. The P. aeruginosa strain PAO1 was grown in the iron-limited medium TSB-DC with or without 10% (v/v) ABS. The presence of 10% ABS reduced PAO1 growth, but despite this reduction, the cultures reached early exponential phase at 4 h and early stationary phase at 8 h in both media. Accordingly, we determined the PAO1 transcriptome in both media at these two specific time points. To standardize the comprison, we adjusted the cultures to the same optical density at 600 nm (biomass) by diluting with fresh TSB-DC PAO1 grown in TSB-DC to the same OD as PAO1 grown in TSB-DC/ABS. We obtained the transcriptome profile of 5,552 genes representing the complete P. aeruginosa PAO1 genome.
2012-07-08 | E-GEOD-30698 | biostudies-arrayexpress