|
| Status |
Public on May 15, 2024 |
| Title |
USA100 untreated biol rep A |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Staphylococcus aureus |
| Characteristics |
tissue: bacterial cells
cell line: USA100
treatment: untreated
|
| Treatment protocol |
The cell suspension (3 mL) was aliquoted into sterile culture tubes, and loratadine was added to the appropriate concentration (≤25% of the compound MIC = 50 uM). Compound 8 was added to a separate culture tube to the appropriate concentration (≤25% of the compound MIC = 25 uM). Oxacillin was added to a separate culture tube at 4 ug/mL. Cotreatment consisted of both oxacillin (4 ug/mL) and loratadine (50uM) or oxacillin (4 ug/mL) and compound 8 (25uM). Untreated cultures served as negative controls. These treatments continued for 1 hour while in the shaking incubator.
|
| Growth protocol |
S. aureus USA100 (BAA-1753) was purchased from American Type Culture Collection. Cultures were grown overnight in CAMHB at 37 °C with shaking. Mid-log-phase cultures were diluted to 5 × 105CFU mL–1in CAMHB.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from 3mL of culture using a Qiagen RNeasy kit and Thermo's Turbo DNase kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Un_A
|
| Data processing |
Quality control of resulting reads included removing adapter-containing reads, removing reads where “N” was > 10%, and removing low-quality reads where the quality value of over 50% of the bases was ≤ 5.
The remaining reads were mapped to the reference genome (Staphylococcus aureus subsp. aureus N315, NC_002745.2) using Bowtie2.
Gene expression levels were quantified as fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) and averaged among biological triplicate samples.
Pearson correlation analysis quantified the correlation among biological triplicates.
Assembly: Staphylococcus aureus subsp. aureus N315, NC_002745.2
Supplementary files format and content: An Excel spreadsheet for all treatment comparison groups that contain all analyzed replicates, gene information, read counts, fpkm, log2fold change and adjusted pvalues
|
| |
|
| Submission date |
May 08, 2024 |
| Last update date |
May 15, 2024 |
| Contact name |
Heather Bennett Miller |
| E-mail(s) |
[email protected]
|
| Organization name |
High Point University
|
| Department |
Chemistry
|
| Street address |
One University Parkway
|
| City |
High Point |
| State/province |
NC |
| ZIP/Postal code |
27268 |
| Country |
USA |
| |
|
| Platform ID |
GPL27158 |
| Series (1) |
| GSE267020 |
Novel anti-virulence compounds disrupt exotoxin expression in MRSA |
|
| Relations |
| BioSample |
SAMN41264678 |
| SRA |
SRX24495903 |
