|
| Status |
Public on Jul 10, 2017 |
| Title |
UAMS1_wildtype_6h |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells, pelleted
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: UAMS-1
genotype: wild-type
growth medium: TSB (dextrose depleted)
growth conditions: 6h/37°C/+
|
| Treatment protocol |
Samples were stored at -80°C prior to RNA extraction
|
| Growth protocol |
Strains were grown in TSB medium (dextrose depleted) at 37°C with shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion DNA-free
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
total RNA, rRNA-depleted
|
| Data processing |
Raw data files (.sff) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The accession number for the Genbank genome file used as references was NC_002952
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format
|
| |
|
| Submission date |
Jan 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ronan Kevin Carroll |
| E-mail(s) |
carrolr3@ohio.edu
|
| Phone |
740-593-2201
|
| Organization name |
Ohio University
|
| Department |
Biological Sciences
|
| Street address |
107 Irvine Hall
|
| City |
Athens |
| State/province |
OHIO |
| ZIP/Postal code |
45701 |
| Country |
USA |
| |
|
| Platform ID |
GPL19476 |
| Series (1) |
| GSE77400 |
The Staphylococcus aureus nitric oxide synthase (saNOS) modulates respiratory metabolism and cell physiology |
|
| Relations |
| BioSample |
SAMN04448445 |
| SRA |
SRX1553733 |
