|
| Status |
Public on Sep 26, 2023 |
| Title |
BSS1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
treatment: BSS treatment 1
|
| Treatment protocol |
Bacterial cells were grown in CAMHB untill reached OD600 =1 and BSS(16 μM) , eravacycline(0.5μM) or the combination was added to the treated culture. After 30 minutes, cells were collected for the RNA extraction. Subsequently cells were harvested by centrifugation at 10.000 x g for 1 minute, snap-frozen in liquid nitrogen and stored at -80°C prior to RNA isolation.
|
| Growth protocol |
P.aeruginosa PAO1 were grown in CAMHB medium at 37 degees celcius. Cultures were aerated with shaking 220rpm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell were lysed using glassbead and total RNA was isolated using TRIzol/chlorophorm extraction followed by ethanol and isopropanol precipitation
Standard library preparation protocol of BGI for Illumina RNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
mapping of reads was done using: bowtie2 --local using P.aeruginosa PAO1 as template genome
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
Count values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Assembly: Pseudomonas aeruginosa PAO1 ASM676v1 genomic
Supplementary files format and content: Tab delimited text file
|
| |
|
| Submission date |
Jan 23, 2023 |
| Last update date |
Sep 26, 2023 |
| Contact name |
Anne de Jong |
| E-mail(s) |
anne.de.jong@rug.nl
|
| Phone |
+31 50 363 2047
|
| Organization name |
university of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL28386 |
| Series (1) |
| GSE223542 |
Transcriptomic analysis of Pseudomonas aeruginosa under the treatment of bismuth subsalicylate(BSS), eravacycline or the combination |
|
| Relations |
| BioSample |
SAMN32880543 |
| SRA |
SRX19144473 |
