|
| Status |
Public on Apr 14, 2022 |
| Title |
oxacillin treated replicate B |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell total RNA
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: ATCC 43300
treatment: oxacillin, 4 ug/mL
|
| Treatment protocol |
The cell suspension (3 mL) was aliquoted into sterile culture tubes, and compound 8 was added 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 compound 8 (25uM). Untreated cultures served as negative controls. These treatments continued for 1 hour while in the shaking incubator.
|
| Growth protocol |
S. aureus 43300 was purchased from the American Type Culture Collection. Cultures were grown overnight in CAMHB at 37 °C with shaking. Mid-log-phase cultures were diluted to 5 × 10^5 CFU mL–1 in 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 |
Ox_B
|
| 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 (ATCC 43300) 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.
Genome_build: ATCC 43300
Supplementary_files_format_and_content: *_DEG.txt: Tab-delimited text files for all treatment comparison groups that contain all replicates, gene information, read counts, fpkm, log2fold change and adjusted pvalues.
|
| |
|
| Submission date |
Jan 10, 2022 |
| Last update date |
Apr 14, 2022 |
| 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) |
| GSE193395 |
Brominated carbazole's antibiotic adjuvant effects in MRSA 43300 |
|
| Relations |
| BioSample |
SAMN24811416 |
| SRA |
SRX13705478 |
