|
| Status |
Public on Jun 07, 2024 |
| Title |
RB50 2% O2 sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
RB50
|
| Organism |
Bordetella bronchiseptica |
| Characteristics |
strain: RB50
genotype: WT
treatment: 2% O2
|
| Treatment protocol |
Cultures were grown in different atmospheric conditions: ambient air, 5% O2, 2% O2, or 5% CO2
|
| Growth protocol |
Overnight cultures were backdiluted to 1 OD600/mL in Stainer Scholte medium. These cultures were then grown for 4 hours at 37C shaking at 225 rpm on an orbital shaker while being exposed to different atmospheric conditions. Bacteria were pelleted, resuspended in RNAlater (Invitrogen AM7020), then stored at -80°C until extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Trizol/chloroform extraction, followed by centrifugation in Phasemaker Tubes (Invitrogen 12183555). The aqueous phase was precipitated in isopropanol, washed in ethanol, and solubilized in RNase-free water. Samples were then cleaned using RNAeasy column purification (Qiagen 74104).
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Read mapping was performed using HISAT2
Read quantification was performed using featureCounts
Read counts were loaded into R, then normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm
Differential expression analysis between our different conditions (5% O2 vs ambient air, 2% O2 vs ambient air, and 5% CO2 vs ambient air) was performed using edgeR’s glmQLFTest.
Assembly: NC_002927.3
Supplementary files format and content: HISAT2 reads
Supplementary files format and content: .bam files
|
| |
|
| Submission date |
May 29, 2024 |
| Last update date |
Jun 07, 2024 |
| Contact name |
Peggy A. Cotter |
| E-mail(s) |
[email protected]
|
| Organization name |
UNC Chapel Hill
|
| Department |
Microbiology & Immunology
|
| Street address |
125 Mason Farm Rd, 6101 Marsico Hall Cb7290
|
| City |
Chapel Hill |
| State/province |
North Carolina |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL34533 |
| Series (1) |
| GSE268598 |
Effect of oxygen and carbon dioxide on gene expression in Bordetella bronchiseptica strain RB50 |
|
| Relations |
| BioSample |
SAMN41582113 |
| SRA |
SRX24739102 |
