|
| Status |
Public on Nov 19, 2020 |
| Title |
TRQ-STA3, biological replicate3 |
| Sample type |
SRA |
| |
|
| Source name |
Stationary phase bacterial culture of PAO1 treated by TRQ
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
treatment: TRQ-treated PAO1 strain in lB medium
growth phase: Stationary phase
|
| Treatment protocol |
Bacterial cells were collected and kept on ice to extract RNA.
|
| Growth protocol |
Bacterial cells were grown for 6 (EXP) and 12 (STA) hr to reach exponential phase at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5 μg of total RNA. Briefly, rRNA was removed by RiboZero rRNA removal kit (Epicenter), fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200~300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Gene expression data from TRQ-treated PAO1 grown till stationary phase
|
| Data processing |
The raw paired end reads were trimmed and quality controlled by Trimmomatic with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper software
To identify DEGs (differential expression genes) between two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. The method edgeR was used for differential expression analysis
Genome_build: Pseudomonas aeruginosa PAO1
|
| |
|
| Submission date |
Dec 10, 2019 |
| Last update date |
Nov 19, 2020 |
| Contact name |
Qing Wei |
| E-mail(s) |
vubwqing@hotmail.com
|
| Organization name |
Institute of Microbiology, Chinese Academy of Sciences
|
| Lab |
Biofilm Research Group
|
| Street address |
NO.1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL18644 |
| Series (1) |
| GSE141753 |
Transcriptional responses of Tanreqing treated Pseudomonas aeruginosa cells |
|
| Relations |
| BioSample |
SAMN13523627 |
| SRA |
SRX7299350 |
