|
| Status |
Public on Mar 31, 2010 |
| Title |
Bc14579 SH500µg/ml t30_t0 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
SH500_t30
|
| Organism |
Bacillus cereus ATCC 14579 |
| Characteristics |
treatment_protocol: OD600 0.5 exposed to Sodium hypochlorite 500 µg/ml for 30 min
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted as described by van Schaik et al., 2004
|
| Label |
Cy3
|
| Label protocol |
Complementary DNA was synthesized and labeled using 15 μg of total RNA, and the CyScribe Post-Labeling kit (Amersham Biosciences Europe GmbH) according to the supplier's instructions.
|
| |
|
| Channel 2 |
| Source name |
SH500_t0
|
| Organism |
Bacillus cereus ATCC 14579 |
| Characteristics |
treatment_protocol: OD600 0.5 exposed to Sodium hypochlorite 500 µg/ml for 0 min
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted as described by van Schaik et al., 2004
|
| Label |
Cy5
|
| Label protocol |
Complementary DNA was synthesized and labeled using 15 μg of total 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 |
Lowess-normalization, performed in Feature Extract, Agilent. Subsequently normalized data was processed with the Vampire webbased microarray suite.
|
| |
|
| Submission date |
Oct 29, 2009 |
| Last update date |
Mar 31, 2010 |
| Contact name |
Mara Ceragioli |
| E-mail(s) |
mara.ceragioli@unitn.it
|
| Phone |
0031 317 484983
|
| Fax |
0031 317 484978
|
| Organization name |
WUR
|
| Department |
Food Microbiology LAb
|
| Street address |
Bomenweg
|
| City |
Wageningen |
| ZIP/Postal code |
6700 EV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9493 |
| Series (1) |
| GSE18807 |
Comparative transcriptome and phenotype analysis of Bacillus cereus in response to disinfectant treatments |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
log2 ratio (green processed signal / red processed signal) |
| 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 |
ratio red processed signal / green processed signal |
| INV_VALUE |
log2 ratio (red processed signal / green processed signal) |
