|
| Status |
Public on Apr 25, 2016 |
| Title |
S_aureus_TSB |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells, pelleted
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: USA300 Houston
genotype: wild-type
growth medium: TSB
growth conditions (time/temp/shaking): 3h/37°C/+
|
| 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 Ambio Turbo DNA-free kit
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 |
rRNA-depleted
|
| Data processing |
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The genome files used as references for each sample were: S_aureus_TSB: https://dx.doi.org/10.6084/m9.figshare.2061132.v1; S_epidermidis_TSB: https://dx.doi.org/10.6084/m9.figshare.2072890; S_carnosus_TSB: https://dx.doi.org/10.6084/m9.figshare.2072890
Supplementary_files_format_and_content: Expression values calculated for small non-coding transcripts are presented as RPKM values in excel format
|
| |
|
| Submission date |
Feb 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Andy Weiss |
| Organization name |
University of South Florida
|
| Department |
Department of Cell Biology, Microbiology and Molecular Biology
|
| Lab |
Shaw Lab
|
| Street address |
4202 East Fowler Avenue, ISA2015
|
| City |
Tampa |
| State/province |
Florida |
| ZIP/Postal code |
33620-5150 |
| Country |
USA |
| |
|
| Platform ID |
GPL19476 |
| Series (1) |
| GSE77567 |
Transcriptomic Analysis of Staphylococcal sRNAs: Insights into Species Specific Adaption and the Evolution of Pathogenesis |
|
| Relations |
| BioSample |
SAMN04480501 |
| SRA |
SRX1565201 |
