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

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

PROVIDER: PRJNA576918 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10259076_1.fastq.gz	Fastqsanger.gz
	SRR10259076_2.fastq.gz	Fastqsanger.gz
	SRR10259077_1.fastq.gz	Fastqsanger.gz
	SRR10259077_2.fastq.gz	Fastqsanger.gz
	SRR10259078_1.fastq.gz	Fastqsanger.gz

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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 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 DATS-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 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:

2021-12-31 | GSE178622 | 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

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

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

| PRJNA892976 | ENA

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

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

| PRJNA739737 | ENA

P. aeruginosa PAO1 WT and PA2663 biofilm cells

Project description:P. aeruginosa PAO1 PA2663-UW expression in biofilm cells relative to P. aeruginosa PAO1 WT-UW expression in biofilm cells. All samples cultured in LB with glass wool. Keywords: Mutation

2008-05-29 | GSE7968 | 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

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

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

| PRJNA486815 | ENA

P. aeruginosa PAO1 PA2663 mutant vs. wild type strain

Project description:P. aeruginosa PAO1 wild type and PA2663 mutant strains expression in biofilm cells relative to P. aeruginosa PAO1 wild type strain expression in biofilm cells. All samples cultured in LB with glass wool Keywords: Biofilm

2008-02-22 | GSE9255 | GEO

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