|
| Status |
Public on Mar 14, 2019 |
| Title |
SAUSA300_LAC_agr_KO |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells, pelleted
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: LAC
genotype: agr operon deletion strain
growth medium: TSB
growth conditions: 5h/37°C
|
| Treatment protocol |
Samples were stored at -80°C prior to RNA extraction.
|
| Growth protocol |
Overnight S. aureus cultures were used to inoculate fresh tryptic soy broth and grown for 3 hours. These exponentially growing cultures were subsequently used to seed fresh TSB medium at OD600 0.05. Test cultures were grown for 5 hours and 5 mL of cells were harvested for RNA isolation.
|
| 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 kit. Total RNA was enriched for mRNA using MicrobExpress kit and Illumina RiboZero rRNA removal kit for Gram-positive bacteria.
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 exported from Ion Torrent Server using File Exporter
Raw data files (.fastq) were imported into Qiagen Bioinformatics software platform for analysis and adapters trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values and fold change for filtered reads were caculated using "RNA-Seq Analysis" function with experimental fold change feature in Qiagen Bioinformatics software
Expression values and fold change were normalized by quantile normalization
Normalized expression values and fold change comparisons were exported in excel format
Genome_build: NC_007793.1
Supplementary_files_format_and_content: Expression values calculated for each gene are presented as normalized RPKM values
|
| |
|
| Submission date |
Oct 22, 2018 |
| Last update date |
Mar 14, 2019 |
| Contact name |
Lindsey N Shaw |
| Organization name |
University of South Florida
|
| Department |
CMMB
|
| Street address |
4202 E Fowler Avenue
|
| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33620 |
| Country |
USA |
| |
|
| Platform ID |
GPL19476 |
| Series (1) |
| GSE121625 |
Transcriptomic analysis of agr-deficient Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN10268418 |
| SRA |
SRX4913543 |
