|
| Status |
Public on Apr 10, 2013 |
| Title |
synthetic nasal medium (SNM), biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
synthetic nasal medium (SNM) at OD578nm 0.02
|
| Organism |
Staphylococcus aureus |
| Characteristics |
strain: USA300
|
| Treatment protocol |
Cells were harvested by centrifugation at an OD578 of 0.02 after RNA was stabilised in the culture with 1/9 volume of ice cold phenol:ethanol mixture (1:9). Cell pellets were washed with ice cold ethanol:acetone (1:1), and a final washing and stabilistaion step was made with RNAprotect bacteria reagent (QIAGEN). Finally cells were immediately frozen at -80°C.
|
| Growth protocol |
Basic medium (BM composed of 1% tryptone, 0.5% yeast extract, 0.5% NaCl, 0.1% K2HPO4 x H2O, and 0.1% glucose) or a chemically defined synthetic medium (SNM) were inoculated with bacterial over-night cultures in SNM at an OD578 of 0.005 and cultivated aerobically with vigorous shaking at 37°C (baffled Erlenmeyer flasks on shaker).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cells were lysed in 100 µl TE buffer containing 10 µl lysostaphin (2 mg/ml) and incubated for 3 min at room temperature. After the addition of 350 µl RLT buffer (RNeasy Kit, QIAGEN GmbH, Germany) cells were lysed with 0.2 ml zirconia-silica beads in a homogenizer and RNA was purified with the RNeasy Kit according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
cDNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA (GeneChip Expression Analysis Technical Manual, Chapter 4 Prokaryotic; 702232, Rev.3). cDNA were labeled with GeneChip® DNA Labeling Reagent (Affymetrix P/N 900542).
|
| |
|
| Hybridization protocol |
Hybridization of cDNA and following washing and staining of GeneChips were carried out according to standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, Chapter 6 Prokaryotic; 702232, Rev.3).
|
| Scan protocol |
GeneChips were scanned using a GeneChip® Scanner 3000 (Affymetrix; P/N 00-00212)
|
| Description |
Gene expression data of aerobic S. aureus cultures in exponential phase of growth
|
| Data processing |
The data were analyzed with GCOS version 1.1 using Affymetrix default analysis settings.
|
| |
|
| Submission date |
Jan 24, 2013 |
| Last update date |
Apr 10, 2013 |
| Contact name |
Bernhard Krismer |
| E-mail(s) |
bernhard.krismer@med.uni-tuebingen.de
|
| Organization name |
University of Tuebingen
|
| Department |
IMIT
|
| Lab |
Prof. A. Peschel
|
| Street address |
Elfriede-Aulhorn-Str. 6
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1339 |
| Series (1) |
| GSE43712 |
Gene expression in synthetic nasal medium |
|
