|
| Status |
Public on Feb 09, 2008 |
| Title |
13501835 - Plant e2 exp1 vs Plant eH exp1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Plant eH exp1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Arabidopsis thaliana (burren) - dev.stage (Boyes et al. Plant Cell 2001):1.08,boyes
|
| Treatment protocol |
Name:Inoculated eH - biotic stress - pathogen infection,isolate eh:. Inoculation was performed by applying 1mL of resting spore suspension (107 spores.ml-1) to the crown of each 7-days-old seedling. Experiments were done in a climatic chamber with 16 hours light at 22degre Celsius and 8 hours dark at 19degre Celsius.
|
| Growth protocol |
whole plant - Media=[2/3 compost, 1/3 vermiculite] mix sterilized by autoclave Temperature=22°C day,19°C night Light=16 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Plant eH exp1:10ug.
|
| Label |
Cy5
|
| Label protocol |
labelling , amplification=, .
|
| |
|
| Channel 2 |
| Source name |
Plant e2 exp1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Arabidopsis thaliana (burren) - dev.stage (Boyes et al. Plant Cell 2001):1.08,boyes
|
| Treatment protocol |
Name:Inoculated e2 - biotic stress - pathogen infection,isolate e2:. Inoculation was performed by applying 1mL of resting spore suspension (107 spores.ml-1) to the crown of each 7-days-old seedling. Experiments were done in a climatic chamber with 16 hours light at 22degre Celsius and 8 hours dark at 19degre Celsius.
|
| Growth protocol |
whole plant - Media=[2/3 compost, 1/3 vermiculite] mix sterilized by autoclave Temperature=22°C day, 19°C night Light=16 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Plant e2 exp1:10ug.
|
| Label |
Cy3
|
| Label protocol |
labelling , amplification=, .
|
| |
|
| |
| Hybridization protocol |
Plant eH exp1 Cy5 / Plant e2 exp1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.
|
| Scan protocol |
GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%
|
| Description |
Characterisation of the transcriptional changes (host genes up- and down-regulated) during the P. brassicae / A. thaliana interaction.
|
| Data processing |
The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.
|
| |
|
| Submission date |
Feb 07, 2008 |
| Last update date |
Feb 08, 2008 |
| Contact name |
Soubigou-Taconnat Ludivine |
| E-mail(s) |
soubigou@evry.inra.fr
|
| Organization name |
INRA
|
| Department |
URGV
|
| Lab |
ADT
|
| Street address |
2 rue gaston crémieux
|
| City |
evry |
| ZIP/Postal code |
91000 |
| Country |
France |
| |
|
| Platform ID |
GPL4346 |
| Series (1) |
| GSE10426 |
Clubroot catma-2: Deciphering the Arabidopsis mechanisms of resistance to clubroot (Plasmodiophora brassicae) |
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