|
| Status |
Public on Nov 14, 2016 |
| Title |
S_aureus_WT |
| 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 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
USA300_WT_vs_rpoZ.xlsx
|
| Data processing |
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis
Expression values for coding genes as well as sRNA track were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Samples were compared using "Set Up Experiment" tool for transcriptomic analysis and standardized via quantile normalization using CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: The S. aureus USA300 FPR3757 genome file was accessed from GenBank (Accesion number:CP000255)
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in excel format
|
| |
|
| Submission date |
Sep 16, 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) |
| GSE87033 |
The ω Subunit Governs RNA Polymerase Stability and Transcriptional Specificity in Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN05784983 |
| SRA |
SRX2172547 |
