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| Status |
Public on Dec 08, 2022 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and geraniol-treated P. aeruginosa PAO1 Transcriptomes |
| Organism |
Pseudomonas aeruginosa PAO1 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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).
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| Overall design |
The mRNA profiles of P. aeruginosa PAO1 (control) and geraniol-treated P. aeruginosa PAO1 were generated by deep sequencing, in triplicate, using Illumina Higseq 2000.
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| Contributor(s) |
Li W, Zhang Z |
| Citation(s) |
37180245 |
| Submission date |
Oct 21, 2022 |
| Last update date |
Aug 04, 2023 |
| Contact name |
Wenru Li |
| E-mail(s) |
liwenru@gdim.cn
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| Phone |
+8613642678264
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| Organization name |
Institute of Microbiology, Guangdong Academy of Sciences
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| Street address |
No.100, Xianliezhong Road
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| City |
Guangzhou |
| ZIP/Postal code |
510070 |
| Country |
China |
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| Platforms (1) |
| GPL28916 |
Illumina NovaSeq 6000 (Pseudomonas aeruginosa PAO1) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA892976 |
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