|
| Status |
Public on Feb 28, 2018 |
| Title |
control_120 |
| Sample type |
SRA |
| |
|
| Source name |
Cell culture
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: 04-02981
accession: ASM2514v1
|
| Treatment protocol |
The bacterial culture was exposed to Ag or AGXX, the culture without addition of any metal sheet served as the control
|
| Growth protocol |
Bacterial cells were grown in Tryptic Soy Broth at 37°C, 150 rpm shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Control 120 min
|
| Data processing |
mapping of reads was done using: bowtie2 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Staphylococcus aureus 04-02981|VERSION Date: 2010/11/05 | GenBank assembly accession: GCA_000025145.2
Supplementary_files_format_and_content: Tab delimited text file
|
| |
|
| Submission date |
Aug 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Anne de Jong |
| E-mail(s) |
anne.de.jong@rug.nl
|
| Phone |
+31 50 363 2047
|
| Organization name |
university of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL20673 |
| Series (1) |
| GSE103064 |
Differential gene expression of S. aureus 04-02981 (MRSA) on exposure to AGXX® |
|
| Relations |
| BioSample |
SAMN07555256 |
| SRA |
SRX3130497 |
