|
Status |
Public on Sep 26, 2023 |
Title |
E2 |
Sample type |
SRA |
|
|
Source name |
Bacterial
|
Organism |
Pseudomonas aeruginosa |
Characteristics |
strain: PAO1 treatment: Eravacycline treatment 2
|
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
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|
|
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 |
SAMN32880540 |
SRA |
SRX19144476 |