|
| Status |
Public on Jun 12, 2023 |
| Title |
PA14_DrsaLDlasR_14_rllas_A |
| Sample type |
SRA |
| |
|
| Source name |
RNASeq of planctonic culture of Pseudomonas aeruginosa UCBPP-PA14 delta rsaL delta lasR pSEVA224::rsaL_long pSEVA644::lasR_antisense treated for 2 h with 0.1 mM IPTG at OD (0.5-0.7)
|
| Organism |
Pseudomonas aeruginosa UCBPP-PA14 |
| Characteristics |
cell line/strains: PA14 delta rsaL delta lasR pSEVA224::rsaL_long pSEVA644::lasR_antisense
|
| Treatment protocol |
Cells harboring plasmid pJN105 were treated with 0.1 % arabinose at OD600 of 1 and harvested at OD600 of 2. Cells harboring plasmids pSEVA224 and pSEVA644 were treated with 0.1 mM IPTG at OD600 of 0.5-0.7 and harvested 2 h later at OD600 of 1.1-1.6.
|
| Growth protocol |
Bacterial subcultures were grown in liquid LB, at 37 °C and 180 rpm shaking. For cells harboring plasmid pJN105, medium was supplemented with gentamicin (50 µg/ml). For cells harboring plasmids pSEVA224 and pSEVA644, medium was supplemented with gentamicin (40 µg/ml) and kanamycin (200 µg/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cell pellets were resuspended in RNAprotect. RNA extraction was done as previously described (Schinner et al., 2020)
NEBNext Ultra II Directional RNA Library Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
start OD600 of 0.05; treated for 2 h with 0.1 mM IPTG at OD (0.5-0.7)
rpg_table_PA14_pSEVA_constructs.csv
|
| Data processing |
Pseudomonas aeruginosa UCBPP-PA14
Reads were mapped using bowtie2 (--very-sensitive-local --no-mixed --no-discordant --fr )
Reference genome: NC_008463.1
Files were converted into bam format using samtools
reads per gene from Pseudomonas aeruginosa UCBPP-PA14 were extracted using featureCounts (-Q 20 --fracOverlap 0.5)
Supplementary_files_format_and_content: reads per gene include antisense mapped reads of lasR and rsaL (using featureCounts options -s 1/2), antisense reads were selected using R environent
|
| |
|
| Submission date |
Jun 12, 2020 |
| Last update date |
Jun 12, 2023 |
| Contact name |
Matthias Preusse |
| Organization name |
Helmholtz Centre for Infection Research
|
| Street address |
Inhoffenstr. 7
|
| City |
Braunschweig |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27892 |
| Series (1) |
| GSE152384 |
Analysis of the organization and expression patterns of the convergent lasR/rsaL gene pair uncovers mutual influence |
|
| Relations |
| BioSample |
SAMN15224340 |
| SRA |
SRX8538407 |
