|
| Status |
Public on Mar 23, 2023 |
| Title |
untreated biol rep A |
| Sample type |
SRA |
| |
|
| Source name |
43300
|
| Organism |
Staphylococcus aureus |
| Characteristics |
cell line: 43300
cell type: bacterial cells
treatment: untreated, DMSO only
|
| 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). Oxacillin was added to a separate culture tube at 4 ug/mL. Cotreatment consisted of both oxacillin (4 ug/mL) and loratadine (50uM). 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 |
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 (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.
Pearson correlation analysis quantified the correlation among biological triplicates. Only one sample out of twelve did not meet the correlation criteria of 0.92 (cotreated biol rep A) and it was removed from subsequent analysis.
Assembly: ATCC 43300 https://genomes.atcc.org/genomes/79691302ed634fef
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 |
Mar 10, 2023 |
| Last update date |
Mar 23, 2023 |
| Contact name |
Heather Bennett Miller |
| E-mail(s) |
hmiller@highpoint.edu
|
| 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) |
| GSE227099 |
Loratadine's antibiotic adjuvant effects in MRSA 43300 |
|
| Relations |
| BioSample |
SAMN33715473 |
| SRA |
SRX19635364 |
