|
| Status |
Public on Sep 06, 2022 |
| Title |
WT_wo_Fe_5 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Staphylococcus aureus subsp. aureus USA300 |
| Characteristics |
bacterial strain: USA300_FPR3757
mutation in strain: None
treatment: None
|
| Treatment protocol |
Cells were treated with 10 µM ferric ammonium sulfate or left untreated.
|
| Growth protocol |
An individual bacterial colony was picked off a plate and grown overnight in tris minimal succinate (TMS) supplemented with 0.4 µM hemin. Cells were sub-cultured to a starting OD600 of 0.01 in iron restricted TMS supplemented with hemin and 1.5 µM transferrin. Cells were grown until mid-log phase at which point cells were treated with 10 µM ferric ammonium sulfate or left untreated for 1 hour before cells were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To extract RNA from frozen S. aureus and hemB S. aureus, cell pellets were washed with TE buffer (pH 8.0) and re-suspended in a Tris-HCl mixture with 1 mg/mL lysostaphin (pH 7.5) to lyse for 1 hour at 37°C. RNA was extracted using an AurumTM Total RNA Mini Kit (BioRAD #7326820).
RNA samples were processed by the Microbial Genome Sequencing Center in Pittsburgh, PA. Ribosomal RNA (rRNA) was depleted (Qiagen FastSelect5S/16S/23S) and cDNA libraries were generated (Qiagen Total Stranded RNA). cDNA libraries were sequenced using NextSeq 550 using a 75bp x 8bp x 8bp setup.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Sequencing reads were mapped to the reference S. aureus USA300 FPR3757 genome in Geneious Prime 2020.1.2 (https://www.geneious.com). Expression analysis and comparisons were performed using DESeq2 (Love MI et al Genome Biol 2014).
Genome_build: Staphylococcus aureus USA300_FPR3757
Supplementary_files_format_and_content: xlsx file format, contains RPKM values and calculated differential expression, fold change and p-values for every transcript.
Supplementary_files_format_and_content: The processed data file contains all replicates combined and the calculations of differential expression/fold changes are based on the comparison with the appropriate control group. Each sheet is named after the corresponding comparison.
|
| |
|
| Submission date |
Sep 14, 2021 |
| Last update date |
Sep 06, 2022 |
| Contact name |
David Heinrichs |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Western Ontario
|
| Street address |
Microbiology and Immunology, 3014 Dental Sciences Building, 1151 Richmond Street
|
| City |
London |
| State/province |
ON |
| ZIP/Postal code |
N6A5C1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL30628 |
| Series (1) |
| GSE184082 |
The iron starvation response of the Staphylococcus aureus hemB small colony variant (SCV) |
|
| Relations |
| BioSample |
SAMN21424561 |
| SRA |
SRX12177673 |
