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Sample GSM249087 Query DataSets for GSM249087
Status Public on May 11, 2008
Title delta sigZ 60 min after ethanol exposure (dZ0met60_1)
Sample type RNA
 
Channel 1
Source name dZ 0
Organism Bacillus cereus ATCC 14579
Characteristics delta sigZ 0 min after ethanol exposure.
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 dZ 60
Organism Bacillus cereus ATCC 14579
Characteristics delta sigZ 60 min after ethanol exposure.
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)
GSE9858 Monitoring the ethanol stress response of a sigZ deletion strain of B. cereus ATCC 14579.

Data table header descriptions
ID_REF
VALUE log2 of PRE_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

Data table
ID_REF VALUE gProcessedSignal rProcessedSignal gMeanSignal rMeanSignal gMedianSignal rMedianSignal gBGMeanSignal rBGMeanSignal gBGMedianSignal rBGMedianSignal PRE_VALUE
2 0.0000 2.10E+01 1.96E+01 5.31E+01 5.70E+01 52.5 57 4.41E+01 5.38E+01 44 54 1
46 0.0000 2.76E+01 2.11E+01 5.46E+01 5.43E+01 53 55 4.46E+01 5.26E+01 44 53 1
105 0.0000 2.65E+01 2.22E+01 5.64E+01 5.33E+01 56.5 52 4.53E+01 5.18E+01 45 51 1
108 0.0000 2.70E+01 2.11E+01 5.26E+01 5.56E+01 51 56 4.39E+01 5.31E+01 44 53 1
109 0.0000 2.49E+01 2.15E+01 5.25E+01 5.50E+01 53 55 4.47E+01 5.33E+01 45 53 1
176 0.0000 2.85E+01 2.09E+01 5.44E+01 5.58E+01 54.5 55 4.61E+01 5.15E+01 46 51.5 1
212 0.0000 2.95E+01 1.98E+01 5.63E+01 5.41E+01 56 54 4.72E+01 5.22E+01 47 52 1
213 0.0000 3.14E+01 2.16E+01 5.79E+01 5.46E+01 58 55 4.73E+01 5.21E+01 47 52 1
214 0.0000 2.62E+01 1.98E+01 5.82E+01 5.55E+01 58 55 4.63E+01 5.15E+01 46 52 1
224 0.0000 2.82E+01 1.95E+01 5.25E+01 5.63E+01 53 56 4.50E+01 5.31E+01 45 53 1
408 0.0000 2.84E+01 2.33E+01 5.64E+01 5.58E+01 56 55 4.73E+01 5.19E+01 47 52 1
460 0.0000 2.46E+01 2.32E+01 5.07E+01 5.69E+01 51 57 4.56E+01 5.26E+01 45 53 1
530 0.0000 2.81E+01 2.24E+01 5.68E+01 5.51E+01 57 55 4.72E+01 5.21E+01 47 52 1
662 0.0000 2.71E+01 2.10E+01 5.22E+01 5.73E+01 52 57 4.57E+01 5.29E+01 45 53 1
699 0.0000 2.84E+01 2.03E+01 5.39E+01 5.66E+01 54 56 4.59E+01 5.19E+01 46 52 1
712 0.0000 2.76E+01 2.04E+01 5.41E+01 5.60E+01 55 56 4.68E+01 5.20E+01 47 52 1
1072 0.0000 2.80E+01 2.10E+01 5.35E+01 5.44E+01 53.5 54.5 4.52E+01 5.24E+01 45 53 1
1153 0.0000 2.92E+01 2.07E+01 5.53E+01 5.51E+01 56 55 4.74E+01 5.22E+01 47 52 1
1203 0.0000 2.67E+01 2.33E+01 5.83E+01 6.06E+01 59 60 4.61E+01 5.20E+01 46 52 1
1325 0.0000 2.37E+01 2.13E+01 5.83E+01 6.05E+01 59 60 4.63E+01 5.15E+01 46 52 1

Total number of rows: 10698

Table truncated, full table size 972 Kbytes.




Supplementary file Size Download File type/resource
GSM249087.txt.gz 2.5 Mb (ftp)(http) TXT
Processed data included within Sample table
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