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Sample GSM133482 Query DataSets for GSM133482
Status Public on Sep 30, 2006
Title Pathogen_vs_Control_replicate_2
Sample type RNA
 
Channel 1
Source name Diseased Arabidopsis
Organism Arabidopsis thaliana
Characteristics Arabidopsis thaliana col-0, inoculated with Erysiphe cichoracearum, no Si supplementation
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Control Arabidopsis
Organism Arabidopsis thaliana
Characteristics Arabidopsis thaliana col-0, non inoculated, no Si supplementation
Extracted molecule total RNA
Label Cy5
 
 
Hybridization protocol Hybridization was performed following Agilent's oligonucleotide microarray hybridization user's manual and Agilent's in situ Hybridization Plus kit. A volume of 200 µL of combined Cy3- and Cy5-labeled cDNA targets were denatured at 98 °C for 3 min and cooled to room temperature. They were mixed with 50 µL of 10x control targets, followed by the addition of 250 µL of 2x hybridization buffer. The 500 µL of reaction mix was applied to each Agilent 44K Arabidopsis 3 microarray (37,537 features), and hybridized in a hybridization rotation oven at 60 °C for 17 h. The slides were disassembled in 6 x SSC, 0.005% Triton X-102, washed first with 6xSSC, 0.005% Triton X-102 for 10 min at room temperature, then with 0.1 xSSC, 0.005% Triton X-102 for 5 min on ice, and dried using a nitrogen-filled air gun.
Scan protocol The arrays were scanned using a dual-laser DNA microarray scanner (Agilent). The data was then extracted from images with Agilent’s Feature Extraction software 7.5.
Description Supplementary file contains data obtained after scan
Data processing The R software 2.3 and the LIMMA package were used to normalize the microarray data (loess method for within array normalization followed by quantile method for between arrays normalization)
 
Submission date Sep 01, 2006
Last update date Sep 06, 2006
Contact name Florian Chain
E-mail(s) florian.chain@inra.fr
Organization name INRA
Department Institut Micalis
Lab Probihote
Street address Domaine de Vilvert
City Jouy en Josas
ZIP/Postal code 78352
Country France
 
Platform ID GPL2871
Series (1)
GSE5718 The protective role of silicon in the Arabidopsis-powdery mildew pathosystem

Data table header descriptions
ID_REF
VALUE Normalized Log Ratio (Loess followed by quantile)

Data table
ID_REF VALUE
1 -5.6870377109623
2 -1.84193276357339
3 -0.201567448165904
4 -0.290474037296394
5 0.719108903748158
6 -0.0788183701435576
7 -5.45568488903707
8 -0.358359067361997
9 0.73507373735636
10 0.119031367799072
11 0.721303009084751
12 -0.534835825709862
13 -5.46223513230503
14 0.320140997637167
15 0.0836411164567545
16 1.02577638951078
17 -0.673734553489435
18 -0.20114295407107
19 -5.900503387932
20 0.772476415483908

Total number of rows: 39941

Table truncated, full table size 932 Kbytes.




Supplementary file Size Download File type/resource
GSM133482.txt.gz 11.1 Mb (ftp)(http) TXT

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