|
| Status |
Public on Apr 04, 2012 |
| Title |
S.sanguinis_wt_2 |
| Sample type |
RNA |
| |
|
| Source name |
8 hours culture of S.sanguinis SK36
|
| Organism |
Streptococcus sanguinis SK36 |
| Characteristics |
strain: SK36
genotype/variation: wild type
artificial ai2 added: no
|
| Treatment protocol |
Artificial AI-2 precursor was added at two time points, after 5.5 h and 7 h of growth to gain a final concentration of 4.5 µM (with the first addtion) and 9 µM (with the second addition), respectively.
|
| Growth protocol |
Bacterial cells were cultured under anaerobic conditions (10% CO2; 10% H2; 80% N2) at 37°C in chemical defined medium sublemented with 50 mM succrose for 8 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted out of 100 mg harvested cells using the Fast RNA Pro Blue Kit (MP Biomedicals, Solon, Ohio, USA) following manufacturers instructions. Removal of DNA was performed by DNase digenstion for 1 hour at 37°C.
|
| Label |
Cy3
|
| Label protocol |
Labeling with Cy3 was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen®)
|
| |
|
| Hybridization protocol |
Hybridization was executed as recommended by the array user guide (Gene Expression Analysis v 2.0, NimbleGen®)
|
| Scan protocol |
Scanning was performed with the DNA Microarray Scanner (Agilent) at a resolution of 5 µm and NimbleScanTM version 2.4 software
|
| Description |
This sample is of wild-type S. sanguinis SK36.
|
| Data processing |
The raw data (.pair file) were checked for inhomogenous hybridization and probes with a high intensity caused by wash artefacts were deleted. Probes not belonging to S. sanguinis SK36 or RANDOM were excluded from analysis. The remaining probes were quantile normalized, background corrected, and sumarized with NimbleScan Software RMA, and subsequently analysed with GeneSpring GX 11.0, Agilent Technologies. Gene-signal intensities are quantile normalized, and background corrected with RMA over all samples, averaged of three technical on chip replikates, and displayed in log2 scale.
|
| |
|
| Submission date |
Apr 03, 2012 |
| Last update date |
Apr 04, 2012 |
| Contact name |
Sylvio Redanz |
| E-mail(s) |
sylvio.redanz@med.uni-rostock.de
|
| Phone |
0381 494 5939
|
| Organization name |
hospital university rostock
|
| Department |
Institute of microbiology, virology and hygiene
|
| Lab |
medical microbiology
|
| Street address |
Schillingallee 70
|
| City |
Rostock |
| State/province |
Mecklenburg Vorpommern |
| ZIP/Postal code |
18057 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15399 |
| Series (1) |
| GSE37007 |
Heterologous expression of sahH reveals that biofilm formation is autoinducer-2 independent in Streptococcus sanguinis, but is associated with an intact AMC |
|
