|
Status |
Public on Oct 10, 2015 |
Title |
Mid-log cells compared to 24 hour biofilm |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
mid-logarithmic phase cells sample 1
|
Organism |
Bacillus cereus ATCC 14579 |
Characteristics |
strain: ATCC 14579
|
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 |
24 hour biofilm cells sample 2
|
Organism |
Bacillus cereus ATCC 14579 |
Characteristics |
strain: ATCC 14579
|
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 100% 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 11, 2010 |
Last update date |
Oct 10, 2015 |
Contact name |
Janneke Wijman |
Organization name |
Wageningen UR
|
Lab |
Food Microbiology
|
Street address |
Bomenweg 2
|
City |
Wageningen |
ZIP/Postal code |
6701 HD |
Country |
Netherlands |
|
|
Platform ID |
GPL7680 |
Series (2) |
GSE24619 |
Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus ATCC 14579 |
GSE24635 |
Comparative transcriptome analysis of biofilm and planktonic cells of Bacillus cereus |
|
Data table header descriptions |
ID_REF |
|
VALUE |
log2 ratio (mid-log cells/ 24h biofilm) |
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 |