|
Status |
Public on Apr 08, 2022 |
Title |
HOU_xdrA |
Sample type |
SRA |
|
|
Source name |
bacterial cells, pelleted
|
Organism |
Staphylococcus aureus |
Characteristics |
strain: HOU/TCH1516 genotype: xdrA transposon mutant strain growth medium: TSB growth conditions: 5h/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 5 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 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 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 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: The accession number for the Genbank genome file used as references was NC_010079.1 Supplementary_files_format_and_content: Expression values calculated for each gene are presented as TPM values in excel format
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|
|
Submission date |
May 17, 2021 |
Last update date |
Apr 08, 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) |
GSE174558 |
Transcriptomic analysis of xdrA difficient Staphylococcus aureus |
|
Relations |
BioSample |
SAMN19233474 |
SRA |
SRX10912673 |