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| Status |
Public on Dec 08, 2022 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAS71 and LVX-treated P. aeruginosa PAS71 Transcriptomes |
| Organism |
Pseudomonas aeruginosa |
| 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 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).
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| Overall design |
The mRNA profiles of P. aeruginosa PAS71 (control) and LVX-treated P. aeruginosa PAS71 were generated by deep sequencing, in triplicate, using Illumina Higseq 2000.
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| Contributor(s) |
Li W, Zhang Z |
| Citation(s) |
36620018 |
| |
| Submission date |
Nov 07, 2022 |
| Last update date |
Jan 13, 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) |
| GPL18644 |
Illumina HiSeq 2000 (Pseudomonas aeruginosa) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA898911 |
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