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Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and DATS-treated P. aeruginosa PAO1 Transcriptomes

ABSTRACT: 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 DATS-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 1.0E8 CFU/mL. Diallyl trisulfide was then added at a concentration of either 0 (control) or 0.63 μl/mL, respectively, in triplicate. All nine 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: The transcriptome sequencing data of control and DATS-treated groups were compared and analyzed in the form of the following: control vs DATS. The details of the differentially expressed genes among the two groups showed that the amount of differential expressed genes between control group and DATS-treated group was high (total 5572, up-regulated 929, down-regulated 1432). Conclusions:

ORGANISM(S): Pseudomonas aeruginosa PAO1

PROVIDER: GSE178622 | GEO | 2021/12/31

REPOSITORIES: GEO

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Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and geraniol-treated P. aeruginosa PAO1 Transcriptomes

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 geraniol-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 1.0E8 CFU/mL. Diallyl trisulfide was then added at a concentration of either 0 (control) or 0.63 μl/mL, respectively, in triplicate. All nine 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: The transcriptome sequencing data of control and geraniol-treated groups were compared and analyzed in the form of the following: control vs geraniol. The details of the differentially expressed genes among the two groups showed that the amount of differential expressed genes between control group and geraniol-treated group was high (total 5788, up-regulated 1169, down-regulated 852).

2022-12-08 | GSE216316 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and farnesol-treated P. aeruginosa PAO1 Transcriptomes

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

Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and diallyl disulphide-treated P. aeruginosa PAO1 Transcriptomes

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 diallyl disulphide-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis. Methods: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 108 CFU/mL. Then DDS was added, with its concentrations were 0 (as control, three biological repeats numbered A1, A2, and A3) and 0.64 mg/mL (three biological repeats numbered B1, B2, and B3) separately, both with a triplicate. All the six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 150 rpm for 5 hours. The cells were then sampled and centrifuged from the three control groups and three DDS treatment groups, respectively. The cell precipitates in the control and DDS-treated groups were quickly separately frozen at -80 ºC. Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol. Results: The RNA sequencing results revealed that a large number of genes in P. aeruginosa PAO1 were differentially expressed after DDS treatment. More than three thousands of genes were differentially expressed, with either up regulated (1649 genes) or down regulated (1725 genes) more than two-fold. Conclusions:

2018-08-21 | GSE118801 | GEO

iTRAQ dataset of Pseudomonas aeruginosa PAO1 following dially disulfide treatment

Project description:To establish the effect of DADS on the P. aeruginosa proteome, 50-mL LB medium samples were inoculated at 108 CFU/mL with exponential growth phase P. aeruginosa PAO1. DADS was then added at a concentration of 0 (control) or 0.64 mg/mL, in triplicate. The six experimental groups were incubated for 5 h in a water bath shaker at 37 ºC with a shaking rate of 180 rpm. Cells from the three control groups and three DADS treatment groups were then sampled and centrifuged. The cell precipitate from each experiment group was snap-frozen at -80 ºC.

2019-01-24 | PXD011144 | Pride

RNA Seq of Pseudomonas aeruginosa PAO1 exposed to DAS and DAE

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

Pseudomonas aeruginosa PAO1 response to sphingomyelin

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

Transcriptional response to 2-oxoglutarate (alpha-ketoglutarate) in Pseduomonas aeruginosa PAO1

Project description:The transcriptome of P. aeruginosa PAO1 in the presence of extracelluar 2-oxoglutarate at a concentration of 20 mM. We determined the transcriptional response of P. aeruignosa PAO1 to extracellular 2-oxoglutarate.

2014-02-15 | GSE54032 | GEO

Transcriptional response of Pseudomonas aeruginosa PAO1 to NaClO

Project description:In this experiment the transcriptional response of the opportunistic human pathogen Pseudomonas aeruginosa to sublethal concentrations of NaClO was investigated. To this aim, four independent cultures of P. aeruginosa PAO1 grown in minimal medium BM2 were treated with NaClO (2 ug/ml) for 1 h at 37 C followed by RNA extraction and microarray analysis. Untreated cultures served as controls.

2018-04-30 | E-MTAB-2876 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAS81 and LVFX-treated P. aeruginosa PAS81 Transcriptomes

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 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. aeruginosa PAS81 at a concentration of 1.0E8 CFU/mL. Levofloxacin was then added at a concentration of either 0 (control) or 0.125 μg/mL, respectively, 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 LVFX 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: The transcriptome sequencing data of control and LVFX-treated groups were compared and analyzed in the form of the following: control vs LVFX. The details of the differentially expressed genes among the two groups showed that the amount of differential expressed genes between control group and LVFX-treated group was high (total 5581, up-regulated 241, down-regulated 16).

2022-12-08 | GSE189021 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAS71 and LVX-treated P. aeruginosa PAS71 Transcriptomes

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 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. aeruginosa PAS71 at a concentration of 1.0E8 CFU/mL. Levofloxacin was then added at a concentration of either 0 (control) or 0.125 μg/mL, respectively, 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 LVX 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: The transcriptome sequencing data of control and LVX-treated groups were compared and analyzed in the form of the following: control vs LVX. The details of the differentially expressed genes among the two groups showed that the amount of differential expressed genes between control group and LVX-treated group was high (total 5581, up-regulated 241, down-regulated 16).

2022-12-08 | GSE217409 | GEO

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