|
| Status |
Public on Jun 03, 2022 |
| Title |
EI046_1 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: JE2 delta_ofrA
genotype: Mutant
|
| 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 |
SAMN25936109 |
| SRA |
SRX14167950 |
