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Status |
Public on May 30, 2022 |
Title |
UAMS-1 codY, 3h, sample 3 |
Sample type |
SRA |
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Source name |
UAMS-1
|
Organism |
Staphylococcus aureus |
Characteristics |
cell line: UAMS-1 cell type: Bacteria genotype: CodY mutant time: 3 hours
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
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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.
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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 |
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Relations |
BioSample |
SAMN28680273 |
SRA |
SRX15470414 |