NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM607052 Query DataSets for GSM607052
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

Data table
ID_REF VALUE gProcessedSignal rProcessedSignal gMeanSignal rMeanSignal gMedianSignal rMedianSignal gBGMeanSignal rBGMeanSignal gBGMedianSignal rBGMedianSignal PRE_VALUE
1 -4.423586077 4.23E+03 1.97E+02 1.23E+03 6.62E+01 1205.5 65.5 4.21E+01 4.84E+01 42 48 4.66E-02
2 1.6527613 1.77E+01 5.57E+01 6.08E+01 5.14E+01 60 51 4.25E+01 4.78E+01 42 47 3.14E+00
3 -2.27343636 3.50E+03 7.24E+02 1.02E+03 1.04E+02 1006 102 4.30E+01 4.86E+01 43 49 2.07E-01
4 -0.677673734 3.43E+02 2.15E+02 1.62E+02 6.69E+01 162 66 4.27E+01 4.83E+01 43 48 6.25E-01
5 3.319419077 1.88E+02 1.88E+03 1.17E+02 1.81E+02 116 180.5 4.26E+01 4.80E+01 43 48 9.98E+00
6 3.137017801 2.90E+03 2.55E+04 8.19E+02 1.94E+03 822 1846 4.21E+01 4.85E+01 42 48 8.80E+00
7 1.04109251 2.95E+03 6.08E+03 8.48E+02 4.93E+02 839 493 4.24E+01 4.82E+01 42 48 2.06E+00
8 -4.880291902 4.92E+03 1.67E+02 1.43E+03 6.41E+01 1410 64 4.29E+01 4.87E+01 43 48 3.40E-02
9 -5.814063127 4.54E+03 8.06E+01 1.33E+03 5.78E+01 1345.5 58 4.27E+01 4.89E+01 42 49 1.78E-02
10 -3.997962135 1.03E+04 6.42E+02 2.82E+03 9.84E+01 2785.5 98.5 4.27E+01 4.85E+01 42 48 6.26E-02
11 -0.621561062 4.56E+02 2.96E+02 1.94E+02 7.26E+01 188 72 4.23E+01 4.81E+01 42 48 6.50E-01
12 0.590054423 1.44E+03 2.16E+03 4.54E+02 2.06E+02 454 206 4.19E+01 4.82E+01 42 48 1.51E+00
13 1.496907848 2.10E+01 5.92E+01 6.87E+01 5.49E+01 68 55 4.26E+01 4.77E+01 42.5 48 2.82E+00
14 1.697043845 1.86E+01 6.03E+01 6.73E+01 5.24E+01 67 52 4.32E+01 4.88E+01 43 49 3.24E+00
15 -5.831780582 5.03E+03 8.83E+01 1.47E+03 5.86E+01 1450.5 59 4.32E+01 4.84E+01 43 48 1.76E-02
16 1.441839162 8.53E+03 2.32E+04 2.09E+03 1.93E+03 2036 1879 4.29E+01 4.87E+01 43 48 2.72E+00
17 -0.421292106 1.78E+03 1.33E+03 5.49E+02 1.47E+02 545 148 4.27E+01 4.88E+01 42.5 48 7.47E-01
18 2.104651727 4.09E+01 1.76E+02 7.48E+01 6.50E+01 75 64 4.28E+01 4.86E+01 43 49 4.30E+00
19 0.785679855 1.57E+03 2.70E+03 4.87E+02 2.45E+02 491 243 4.26E+01 4.85E+01 43 48 1.72E+00
20 -7.201387651 1.62E+04 1.10E+02 4.49E+03 6.03E+01 4436 59.5 4.30E+01 4.87E+01 43 49 6.79E-03

Total number of rows: 10806

Table truncated, full table size 1006 Kbytes.




Supplementary file Size Download File type/resource
GSM607052.txt.gz 2.9 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap