|
| Status |
Public on Feb 07, 2024 |
| Title |
MexEF oprN efflux pump mutant |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
tissue: bacteria
cell line: PA14
genotype: mexS mutant
|
| Growth protocol |
Overnight cultures of wildtype PA14 or mutant strains grown 16h in LB broth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultures were pelleted at 4°C, resuspended in Trizol (Ambion 10296010), and incubated at 65°C before addition of chloroform. The aqueous layer was collected and RNA was isolated using a mirVana RNA extraction kit (ThermoFisher AM1560). DNAse treatment was performed on RNA using recombinant DNase I (Sigma-Aldrich 04716728001).
RNA samples were sent to Seq Center (Pittsburg, PA) for sequencing using the Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion.
Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.1.5)
Assembly: Read mapping was performed with HISAT21. Read quantification was performed using Subread’s feature Counts2 functionality.
Supplementary files format and content: HISAT2 output is included as Counts.xlsx
|
| |
|
| Submission date |
Dec 11, 2023 |
| Last update date |
Feb 07, 2024 |
| Contact name |
Connor Chain |
| E-mail(s) |
[email protected]
|
| Organization name |
Princeton University
|
| Street address |
Lewis Thomas Lab
|
| City |
Princeton |
| ZIP/Postal code |
08540 |
| Country |
USA |
| |
|
| Platform ID |
GPL33271 |
| Series (1) |
| GSE249862 |
A novel inhibitor of P. aeruginosa folate metabolism exploits metabolic differences for narrow-spectrum antibiotic targeting |
|
| Relations |
| BioSample |
SAMN38760240 |
| SRA |
SRX22854815 |
