|
| Status |
Public on Sep 04, 2024 |
| Title |
WT 6TG 1 |
| Sample type |
SRA |
| |
|
| Source name |
USA300_FPR3757
|
| Organism |
Staphylococcus aureus |
| Characteristics |
tissue: USA300_FPR3757
treatment: 3.125μM R91
|
| Treatment protocol |
Cells treated with the drug received 3.125μM R91 or and equal volume of DMSO for the vehicle control.
|
| Growth protocol |
An overnight culture of WT USA300 was inoculated 1:100 into TSB and grown to an OD600 of 1.5 at 37oC with shaking. 3.125M of R91 was added to the treated cultures and all cultures were then grown for and additional 30 minutes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To extract RNA from frozen 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 QIAGEN RNAEasy kit (QIAGEN ID: 74104)
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 |
| |
|
| Description |
The processed data files has all 3 replicates combined and the calculations of differential expression/fold changesare based on the comparison with the appropriate control group. Each tab is named after what the comparisons are.
|
| Data processing |
Sequencing reads were mapped to the reference S. aureus USA300 FPR3757 genome in Geneious Prime 2022.1 (https://www.geneious.com). Expression analysis and comparisons were performed using DESeq2 (Love MI et al Genome Biol 2014).
Assembly: 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
|
| |
|
| Submission date |
May 02, 2024 |
| Last update date |
Sep 04, 2024 |
| Contact name |
David Heinrichs |
| E-mail(s) |
deh@uwo.ca
|
| 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 |
GPL28116 |
| Series (1) |
| GSE266471 |
Mechanistic Insights and In Vivo Efficacy of Thiosemicarbazones Against Methicillin-Resistant Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN41176755 |
| SRA |
SRX24437127 |
