|
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 |