|
| Status |
Public on May 03, 2021 |
| Title |
AR351_1 |
| Sample type |
SRA |
| |
|
| Source name |
RNASeq of planctonic culture of P. aeruginosa UCBPP-PA14 treated with IC50 of cystobactamid AR351 from OD 0.05 to OD 0.6
|
| Organism |
Pseudomonas aeruginosa UCBPP-PA14 |
| Characteristics |
strain/genotype: PA14 WT
culture type: planctonic
treatement: IC50 of cystobactamid AR351 from OD 0.05 to OD 0.6
|
| Treatment protocol |
Cells were treated with the IC50 of the gyrase inhibitor at OD600 of 0.05 and harvested at OD600 of 0.6.
|
| Growth protocol |
Bacterial subcultures were grown in liquid BM2, at 37 °C and 150 rpm shaking.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial cell pellets were resuspended in RNAprotect. RNA extraction was done as previously described (Schinner et al., 2020)
Libraries were generated according to Shishkin et al., 2015 and Bhattacharyya et al., 2019.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
start OD600 of 0.05; treated with IC50 of cystobactamid AR351 from OD600 of 0.05 to 0.6
|
| Data processing |
Short reads were aligned to the UCBPP-PA14 reference genome NC_008463 using the subread algorithm implemented in R, Rsubread version 1.32.4.
Count estimation was performed using the featureCounts function as implemented in Rsubread.
Genome_build: NC_008463
Supplementary_files_format_and_content: rpg_matrix_PA14_gyr_inhibitors.csv, reads per gene counts for each sample as determined by the featureCounts function
|
| |
|
| Submission date |
Feb 11, 2021 |
| Last update date |
May 03, 2021 |
| Contact name |
Raimo Franke |
| E-mail(s) |
[email protected]
|
| Phone |
-4953161813415
|
| Organization name |
Helmholtz Centre for Infection Research
|
| Department |
Chemical Biology
|
| Street address |
Inhoffenstr. 7
|
| City |
Braunschweig |
| State/province |
Lower Saxony |
| ZIP/Postal code |
38124 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27892 |
| Series (1) |
| GSE166602 |
Targeting bacterial gyrase with cystobactamid, fluoroquinolone and aminocoumarin antibiotics induces distinct molecular signatures in Pseudomonas aeruginosa |
|
| Relations |
| BioSample |
SAMN17864942 |
| SRA |
SRX10075299 |
