|
| Status |
Public on Jan 26, 2017 |
| Title |
LAC_rpiRC |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cells, pelleted
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: AH LAC rpiRC::bursa
genotype: AH LAC carrying the bursa aurealis transposon in the rpiRC gene
growth medium: TSB
growth conditions (time/temp/shaking): 5h/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 |
| |
|
| 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 each gene were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Samples were compared using "Set Up Experiment" tool for transcriptomic analysis 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 |
Jan 27, 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) |
| GSE77301 |
Staphylococcus aureus coordinates leukocidins expression and pathogenesis by sensing metabolic fluxes via RpiRC |
|
| Relations |
| BioSample |
SAMN04444375 |
| SRA |
SRX1549384 |
