|
| Status |
Public on May 30, 2022 |
| Title |
UAMS-1 codY, 6h, sample 1 |
| Sample type |
SRA |
| |
|
| Source name |
UAMS-1
|
| Organism |
Staphylococcus aureus |
| Characteristics |
cell line: UAMS-1
cell type: Bacteria
genotype: CodY mutant
time: 6 hours
|
| Growth protocol |
grown in tryptic soy broth (TSB) (BD Biosciences) supplemented with 0.25% glucose (Sigma-Aldrich). Bacterial cultures were inoculated to an optical density at 600 nm (OD600) of 0.05 from overnight cultures, incubated at 37°C, and aerated at 250 rpm with a flask to medium ratio of 10:1. Bacterial growth was assessed by measuring the OD600. The OD600 for stationary-phase cultures was measured following dilution of cultures in TSB to remain within the linear range of a spectrophotometer. Antibiotics were purchased from Thermo Fisher Scientific and were used at the following concentrations: erythromycin at 5 μg/ml, chloramphenicol at 10 μg/ml, and tetracycline at 10 μg/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Universal Prokaryotic RNA-Seq Prokaryotic AnyDeplete
Libraries were generated using 100 ng of total RNA from each sample and the Universal Prokaryotic RNA-Seq Prokaryotic AnyDeplete (Tecan Genomics, Inc. 900) following the recommended procedure
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
CLC Genomics Workbench version 21.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to the annotated reference genome Staphylococcus aureus strain: UAMS-1(GCA_000788115.1) from NCBI using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Staphylococcus aureus strain: UAMS-1(GCA_000788115.1)
Supplementary files format and content: Excel file that includes Name, Chromosome, Expression n value, TPM, RPKM, Gene Length, Unique gene reads, Total gene reads. The second excel files contains a compiled spreadsheet of all samples with the values used to genereate figures.
|
| |
|
| Submission date |
May 26, 2022 |
| Last update date |
May 30, 2022 |
| Contact name |
MARAT SADYKOV |
| E-mail(s) |
msadykov@unmc.edu
|
| Phone |
4025594953
|
| Organization name |
University of Nebraska Medical Center
|
| Department |
Pathology and Microbiology
|
| Street address |
985900 Nebraska Medical Center
|
| City |
Omaha |
| State/province |
Nebraska |
| ZIP/Postal code |
68198 |
| Country |
USA |
| |
|
| Platform ID |
GPL28116 |
| Series (1) |
| GSE204884 |
Interplay of CodY and CcpA in regulating central metabolism and biofilm formation in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN28680263 |
| SRA |
SRX15470424 |
