|
| Status |
Public on Mar 27, 2022 |
| Title |
VBNC 3 |
| Sample type |
SRA |
| |
|
| Source name |
VBNC
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
treatment: Tobramycin
treatment time: 96 hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction from each sample was completed following the manufacturer's protocol for the Direct-zol RNA Miniprep Kit (Zymo).
rRNA was removed from samples following the manufacturer's protocol for the RiboZero Bacteria Kit (Illumina). Barcoded RNAseq libraries were generated following the manufacturer's protocol for the ScriptSeq v2 Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Data trimmed using Trimmomatic v0.38
Alignment to the reference genome was done using STAR v2.7.10a
Transcript counts obtained with HTSeq v0.12.4
Differential gene expression processed by edgeR v3.24.3
Assembly: GCF_000006765.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Mar 24, 2022 |
| Last update date |
Mar 27, 2022 |
| Contact name |
Devin Sindeldecker |
| E-mail(s) |
devin.sindeldecker@osumc.edu
|
| Organization name |
The Ohio State University
|
| Department |
MI&I
|
| Lab |
Stoodley Lab
|
| Street address |
460 W. 12th Ave.
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL24583 |
| Series (1) |
| GSE199323 |
RNA sequencing of Pseudomonas aeruginosa phoenix colonies, viable but non-culturable colonies (VBNCs), and control samples |
|
| Relations |
| BioSample |
SAMN26926846 |
| SRA |
SRX14595481 |
