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Sample GSM133000 Query DataSets for GSM133000
Status Public on Sep 30, 2006
Title Control_vs_Pathogen_replicate_2
Sample type RNA
Channel 1
Source name Control Arabidopsis
Organism Arabidopsis thaliana
Characteristics Arabidopsis thaliana col-0, non inoculated, no Si supplementation
Extracted molecule total RNA
Label Cy3
Channel 2
Source name Diseased Arabidopsis
Organism Arabidopsis thaliana
Characteristics Arabidopsis thaliana col-0, inoculated with E. cichoracearum, no Si supplementation
Extracted molecule total RNA
Label Cy5
Hybridization protocol • The protocol and conditions used for hybridization, blocking and washing, including any post-processing steps such as staining: 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 raw data obained 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 Aug 31, 2006
Last update date Sep 06, 2006
Contact name Florian Chain
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
VALUE Normalized Log Ratio (Loess followed by quantile)

Data table
1 -5.05320885032255
2 0.367970163015512
3 0.143290211309146
4 1.16492310503210
5 0.23837548142931
6 0.494624566936984
7 -6.33682673598551
8 -0.174424811729355
9 -0.522696410848267
10 0.558952505967656
11 0.637436695551335
12 0.0780602286328742
13 -6.52278174232496
14 -0.206248962192851
15 0.308926331454598
16 -0.836987341207392
17 0.896441808214994
18 0.860000484355337
19 -6.19287867287348
20 0.342974228781232

Total number of rows: 39941

Table truncated, full table size 933 Kbytes.

Supplementary file Size Download File type/resource
GSM133000.txt.gz 10.4 Mb (ftp)(http) TXT

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