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Sample GSM5898126 Query DataSets for GSM5898126
Status Public on Jun 03, 2022
Title JE2_3
Sample type SRA
 
Source name bacteria
Organism Staphylococcus aureus
Characteristics strain: JE2
genotype: WT
Growth protocol 1:100 dilution of independent overnight cultures in RPMI until OD600=0.5
Extracted molecule total RNA
Extraction protocol Rneasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols by the Core Unit Systems Medicine facility at the University Hospital Würzburg
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing cleaning the adaptor sequence from nextseq sequencers using cutadapt
reademption.v.0.4.3 align function with the following parameters (-c -l 20 -q -S -g)
reademption.v.0.4.3 coverage function
reademption.v.0.4.3 gene_quanti function with the following parameters (-l -a -t CDS,tRNA,rRNA,tmRNA,SRP_RNA)
reademption.v.0.4.3 deseq function for DESeq normalization and calculations
Genome_build: NC_007793.1
Supplementary_files_format_and_content: wig files after DESeq2 normalization
 
Submission date Feb 14, 2022
Last update date Jun 03, 2022
Contact name Eslam S. Ibrahim
E-mail(s) eslam.ebrahim@pharma.cu.edu.eg, eslam_samir_ragab.ibrahim@uni-wuerzburg.de
Organization name Institut für Molekulare Infektionsbiologie (IMIB)
Street address Josef-Schneider-Straße 2, Bau D15
City Würzburg
ZIP/Postal code 97080
Country Germany
 
Platform ID GPL24034
Series (1)
GSE196683 The Old Yellow Enzyme OfrA fosters Staphylococcus aureus survival via thiol-dependent redox homeostasis
Relations
BioSample SAMN25936110
SRA SRX14167949

Supplementary file Size Download File type/resource
GSM5898126_JE2_3.wig.gz 15.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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