|
| Status |
Public on May 18, 2016 |
| Title |
S_aureus_3h |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells, exponential growth phase
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain/background: USA300 Houston
genotype/variation: wild-type
growth medium: TSB
growth conditions (time/temp/shaking): 3h/37C/+
growth phase: exponential
|
| 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 for 3h or 16h.
|
| 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 |
Bacterial cells, pelleted
rRNA-depleted
Processed data file: S_aureus_3h_vs_16h.xlsx
|
| Data processing |
Raw data files (.fastq) were imported into the CLC Genomics Workbench software platform for analysis.
Reads corresponding to ribosomal RNA were filtered out and removed.
Expression values for coding genes as well as sRNA track were calculated 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 genome file was accessed from: https://dx.doi.org/10.6084/m9.figshare.2061132.v1
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as RPKM values in Excel format.
|
| |
|
| Submission date |
Jan 26, 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) |
| GSE77242 |
Characterizing the transcriptional adaptation of Staphylococcus aureus to stationary phase growth |
|
| Relations |
| BioSample |
SAMN04440797 |
| SRA |
SRX1548042 |
