|
| Status |
Public on Dec 08, 2022 |
| Title |
RNA of PAS71 LVX3 |
| Sample type |
SRA |
| |
|
| Source name |
Transcriptome of LVX-treated P. aeruginosa PAS71
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAS71
condition: LVX-treated sample
tissue: exponential growth phase culture
|
| Treatment protocol |
LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAS71 at a concentration of 1.0E8 CFU/mL. Levofloxacin were 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.
|
| Growth protocol |
Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAS71, with the bacterial concentration of 1.0E8 CFU/mL. All the three triplicate experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 180 rpm for 5 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells of P. aeruginosa PAS71 were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Assembly: Pseudomonas aeruginosa PAS71
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Nov 07, 2022 |
| Last update date |
Dec 09, 2022 |
| Contact name |
Wenru Li |
| E-mail(s) |
liwenru@gdim.cn
|
| Phone |
+8613642678264
|
| Organization name |
Institute of Microbiology, Guangdong Academy of Sciences
|
| Street address |
No.100, Xianliezhong Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510070 |
| Country |
China |
| |
|
| Platform ID |
GPL18644 |
| Series (1) |
| GSE217409 |
Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAS71 and LVX-treated P. aeruginosa PAS71 Transcriptomes |
|
| Relations |
| BioSample |
SAMN31634908 |
| SRA |
SRX18191473 |
