|
| Status |
Public on Jan 05, 2016 |
| Title |
USA300_TSB |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells, pelleted
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: USA300 Houston
genotype/variation: wild-type
growth medium: TSB
growth conditions (time/temp/shaking): 3h/37°C/+
molecule subtype: total RNA, rRNA-depleted
|
| Treatment protocol |
Samples were stored at -80°C prior to RNA extraction
|
| Growth protocol |
Strains were grown in TSB medium 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 |
| |
|
| 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 numbers for the Genbank genome files used as references were CP000255(for USA300 TSB and USA300 serum), NC_002952 (for UAMS-1 TSB), and NC_007795(for NCTC8325 TSB).
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format
|
| |
|
| Submission date |
Nov 12, 2015 |
| 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) |
| GSE74936 |
Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN04262024 |
| SRA |
SRX1427735 |
