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Sample GSM5319640 Query DataSets for GSM5319640
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
 
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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