|
| Status |
Public on May 27, 2016 |
| Title |
S. epidermidis ET-024 in single species biofilms_replicate E1 |
| Sample type |
SRA |
| |
|
| Source name |
single species biofilms
|
| Organism |
Staphylococcus epidermidis |
| Characteristics |
sample type: S. epidermidis ET-024
|
| Treatment protocol |
N/A
|
| Growth protocol |
Single and dual species biofilms of S. epidermidis ET-024 and S. aureus Mu50 were grown in mueller hinton broth for 24 hours at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RiboPure RNA purification Bacteria Kit
TruSeq stranded library preparation Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
E vs.EM.xls
|
| Data processing |
illumina base-calling
all data were analysed according to the manufacturer's instructions of the CLC Genomic Workbench 8.5.1
reads were mapped to the entire gene with 100 % similarity and no mapping to the flanking regions was allowed
RPKM values were calculated and the p value was determined using edgeR statistics
Supplementary_files_format_and_content: M vs. EM.xls and E vs. EM.xls summarized the gene expression levels in dual species biofilms compared to single species biofilms
|
| |
|
| Submission date |
Mar 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ilse Vandecandelaere |
| E-mail(s) |
ilse_vdcandelaere@hotmail.com
|
| Organization name |
Ghent University
|
| Department |
Pharmaceutical Sciences
|
| Lab |
Laboratory of Pharmaceutical Microbiology
|
| Street address |
Ottergemsesteenweg 460
|
| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL21652 |
| Series (1) |
| GSE79575 |
The mutual effect of Staphylococcus epidermidis and Staphylococcus aureus in dual species biofilms as revealed by RNA-Seq |
|
| Relations |
| BioSample |
SAMN04578313 |
| SRA |
SRX1659815 |
