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Sample GSM201222 Query DataSets for GSM201222
Status Public on Sep 01, 2007
Title Col-0 self comparison experiment 2
Sample type genomic
 
Channel 1
Source name Col-0
Organism Arabidopsis thaliana
Characteristics Arabidopsis thaliana Col-0.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted with a DNeasy Plant Mini Kit (Qiagen, Valencia, CA). Double-stranded DNA was quantified with a Quant-iT dsDNA Broad-Range Assay Kit (Invitrogen, Carlsbad, CA). Quality of genomic DNA prepared was checked by agarose gel electrophoresis.
Label Cy3
Label protocol Genomic DNA (1 micro g) was used for labeling reaction with a Genomic DNA Labeling Kit (Agilent technology) according to direct labeling protocol.
 
Channel 2
Source name Col-0
Organism Arabidopsis thaliana
Characteristics Arabidopsis thaliana Col-0.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted with a DNeasy Plant Mini Kit (Qiagen, Valencia, CA). Double-stranded DNA was quantified with a Quant-iT dsDNA Broad-Range Assay Kit (Invitrogen, Carlsbad, CA). Quality of genomic DNA prepared was checked by agarose gel electrophoresis.
Label Cy5
Label protocol Genomic DNA (1 micro g) was used for labeling reaction with a Genomic DNA Labeling Kit (Agilent technology) according to direct labeling protocol.
 
 
Hybridization protocol Hybridization was performed with an Oligo aCGH/ChIP-on-Chip Hybridization Kit (Agilent Technology) according to the standard protocol, except that Cot-1 DNA was not added to the hybridization solution. After 24-h, the microarray was washed in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent Technology) for 5 min at room temperature, in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent Technology) for 1 min at 37 ˚C and in acetonitrile for 1 min at room temperature.
Scan protocol Immediately after washing the microarray slide was scanned by a DNA microarray scanner (Agilent Technologies).
Description This experiment was performed to assess the reproducablity of the AtMap1 array.
The full-output file was attached as a Supplementary file.
Data processing The signals were quantified and normalized of signals were performed with Feature Extraction Software ver. 9.1 (Agilent Technologies) with default parameters.
 
Submission date Jun 14, 2007
Last update date Aug 14, 2011
Contact name Ikuko Hara-Nishimura
E-mail(s) ihnishi@gr.bot.kyoto-u.ac.jp
Organization name Kyoto University
Department Depertment of Botany
Street address Oiwakecho
City Kitashirakawa, Sakyoku
State/province Kyoto
ZIP/Postal code 606-8602
Country Japan
 
Platform ID GPL5389
Series (1)
GSE8120 Deletion mapping by the AtMap1 array

Data table header descriptions
ID_REF
VALUE log10 ratio (Cy5/Cy3)
gProcessedSignal Normalized signal intensity of Cy3.
rProcessedSignal Normalized signal intensity of Cy5.

Data table
ID_REF VALUE gProcessedSignal rProcessedSignal
1 1.67E-01 1.39E+04 2.05E+04
2 0.00E+00 1.59E+01 1.92E+01
3 0.00E+00 1.55E+01 1.88E+01
4 0.00E+00 1.52E+01 1.83E+01
5 0.00E+00 1.49E+01 1.80E+01
6 0.00E+00 1.46E+01 1.77E+01
7 0.00E+00 1.44E+01 1.74E+01
8 0.00E+00 1.42E+01 1.71E+01
9 0.00E+00 1.41E+01 1.69E+01
10 0.00E+00 1.39E+01 1.67E+01
11 0.00E+00 1.38E+01 1.66E+01
12 2.18E-02 4.38E+02 4.61E+02
13 1.60E-02 1.51E+03 1.57E+03
14 1.20E-01 6.44E+03 8.49E+03
15 6.89E-02 2.23E+01 2.62E+01
16 1.11E-01 9.76E+03 1.26E+04
17 -1.11E-02 9.61E+02 9.36E+02
18 -3.29E-03 4.55E+02 4.51E+02
19 1.97E-03 1.06E+03 1.07E+03
20 -5.06E-02 1.40E+03 1.25E+03

Total number of rows: 45014

Table truncated, full table size 1460 Kbytes.




Supplementary file Size Download File type/resource
GSM201222.txt.gz 12.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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