|
| Status |
Public on Oct 13, 2021 |
| Title |
2A2 |
| Sample type |
SRA |
| |
|
| Source name |
F. tularensis LVS osrR Mutant
|
| Organism |
Francisella tularensis subsp. holarctica LVS |
| Characteristics |
agent: Untreated
genotype: osrR Mutant
experiment: 2A2 Expt. 2
|
| Treatment protocol |
To determine the role of OsrR as a global transcriptional regulator, we profiled the whole transcriptome of the DosrR mutant in the absence or the presence of oxidative stress. The superoxide-generating compound, menadione (final concentration of 1.25mM), was used as an oxidative stress inducer. This concentration of menadione equally affects the viability of wild type F. tularensis LVS or the DosrR mutant. For untreated control, an equal volume of MHB was added, and bacteria were incubated for 1 hour at 37οC with 5% CO2.
|
| Growth protocol |
The Francisella strains were cultured on Mueller-Hinton (MH) chocolate agar plates (BD Life Sciences) and incubated for 48 hours at 37οC and 5% CO2. Individual colonies were selected and inoculated in MH broth (MHB) enhanced with Isovitalex (BD Biosciences), Ferric Pyrophosphate, Glucose, Anhydrous Calcium Chloride, and Hydrous Magnesium Chloride. The bacterial cultures were incubated at 37οC with constant shaking until the bacterial growth reached the mid-log phase (0.2OD).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Invitrogen PureLink RNA mini kit and treated with DNase using Invitrogen TURBO DNA-free Kit
Illumina TruSeq Stranded Total RNA Library Prep kit with RiboZero bacterial rRNA depletion
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
RiboZero bacterial rRNA depletion
|
| Data processing |
gene expression levels were estimated with EDGE-pro (v1.3.1) using Bowtie2 (v2.3.5.1) alignment to F. tularensis reference
differential gene expression was analyzed by DESeq2 (v1.16.1)
Genome_build: NC_007880
Supplementary_files_format_and_content: reads of each gene in an Excel file as used for DESeq2
|
| |
|
| Submission date |
Aug 29, 2021 |
| Last update date |
Oct 13, 2021 |
| Contact name |
Weihua Huang |
| E-mail(s) |
[email protected]
|
| Phone |
2527443748
|
| Organization name |
East Carolina University
|
| Department |
Pathology
|
| Street address |
600 Moye Blvd, Brody 7S-24
|
| City |
Greenville |
| State/province |
North Carolina |
| ZIP/Postal code |
27834 |
| Country |
USA |
| |
|
| Platform ID |
GPL23586 |
| Series (1) |
| GSE183001 |
An AraC/XylS Family Transcriptional Regulator Modulates the Oxidative Stress Response of Francisella tularensis |
|
| Relations |
| BioSample |
SAMN21032510 |
| SRA |
SRX11960705 |
