NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6199281 Query DataSets for GSM6199281
Status Public on May 30, 2022
Title UAMS-1 ccpA, 3h, sample 3
Sample type SRA
 
Source name UAMS-1
Organism Staphylococcus aureus
Characteristics cell line: UAMS-1
cell type: Bacteria
genotype: CcpA mutant
time: 3 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 SAMN28680270
SRA SRX15470417

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap