|
| Status |
Public on May 11, 2008 |
| Title |
delta sigM 60 min after ethanol (dM0met60_2) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
dM 60
|
| Organism |
Bacillus cereus ATCC 14579 |
| Characteristics |
delta sigM 60 min after ethanol .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted as described by van Schaik et al., 2007
|
| Label |
Cy3
|
| Label protocol |
Complementary DNA was synthesized and labeled using 15 μg of total B. cereus RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.
|
| |
|
| Channel 2 |
| Source name |
dM 0
|
| Organism |
Bacillus cereus ATCC 14579 |
| Characteristics |
delta sigM 0 min after ethanol .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted as described by van Schaik et al., 2007
|
| Label |
Cy5
|
| Label protocol |
Complementary DNA was synthesized and labeled using 15 μg of total B. cereus RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.
|
| |
|
| |
| Hybridization protocol |
The target was denatured by boiling for 1 min and immediate cooling on ice prior to hybridization. A total of 200ng of both samples was mixed and applied with the Agilent hybridization buffer to the microarray, according to Agilent manual. Hybridization was performed at 60 °C. The slide was washed according to the Agilent microarray wash protocol.
|
| Scan protocol |
Microarrays were scanned with the Agilent DNA Microarray Scanner, Model G2565BA, according to the Agilent protocol at 50% laser intensity, and 10 micron scan resolution.
|
| Description |
No extra description.
|
| Data processing |
Loewess-normalisation, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite.
|
| |
|
| Submission date |
Dec 12, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Menno van der Voort |
| Organization name |
Wageningen UR
|
| Department |
Agrotechnology and Food Sciences Group
|
| Lab |
Food Microbiology
|
| Street address |
Bomenweg 2
|
| City |
Wageningen |
| ZIP/Postal code |
6703 HD |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL4406 |
| Series (1) |
| GSE9856 |
Monitoring the ethanol stress response of a sigM deletion strain of B. cereus ATCC 14579. |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
-[INV_VALUE] |
| gProcessedSignal |
green processed signal (normalized signal, processed by Feature extract, Agilent) |
| rProcessedSignal |
red processed signal (normalized signal, processed by Feature extract, Agilent) |
| gMeanSignal |
green Mean signal |
| rMeanSignal |
red Mean signal |
| gMedianSignal |
green Median signal |
| rMedianSignal |
red Median signal |
| gBGMeanSignal |
green Background Mean signal |
| rBGMeanSignal |
red Background Mean signal |
| gBGMedianSignal |
green Background Median signal |
| rBGMedianSignal |
red Background Median signal |
| PRE_VALUE |
value of red processed signal / green processed signal |
| INV_VALUE |
log2 of PRE_VALUE |
