|
| Status |
Public on Mar 28, 2022 |
| Title |
HOU_rsp |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells, pelleted
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: HOU/TCH1516
genotype: rsp transposon mutant strain
growth medium: TSB
growth conditions: 15h/37 degrees C
|
| Treatment protocol |
Samples were pelleted and stored at -80°C prior to RNA extraction.
|
| Growth protocol |
Overnight S. aureus cultures were used to inoculate fresh TSB broth and grown for 3 hours. These exponentially growing cultures were subsequently used to seed fresh TSB medium at OD600 0.05. After 15h hour of growth, 5 mL of cells were harvested for RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total bacterial RNA was isolated utilizing the Qiagen RNeasy kit and contaminating DNA was removed by treatment with Ambion TURBO 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 TruSeq Stranded mRNA Kit from Illumina omitting mRNA enrichment steps.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Raw data files (.fastq) were exported from the Illumina BaseSpace Server
Raw data files (.fastq) were imported into Qiagen Bioinformatics software platform (version 11) as paired-end reads for analysis and adapter indices trimmed.
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values and fold change for filtered reads were calculated using RNA-Seq Analysis function (v0.1) with experimental fold change feature in Qiagen Bioinformatics software
Expression values and fold change were normalized by quantile normalization, exported in excel format
Assembly: The accession number for the Genbank genome file used as references was NC_010079.1
Supplementary files format and content: RPKM values and fold change for each gene are presented with excel formatting
|
| |
|
| Submission date |
Mar 28, 2022 |
| Last update date |
Mar 28, 2022 |
| 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 |
GPL28116 |
| Series (1) |
| GSE199593 |
Transcriptomic analysis of rsp deficient Staphylococcus aureus |
|
| Relations |
| BioSample |
SAMN27023049 |
| SRA |
SRX14637559 |
