Affymetrix GeneChip Arabidopsis Genome [ATH1-121501]

Transcriptome analysis of Arabidopsis clubroots and disease resistance of cytokinin oxidase/dehydrogenase gene overexpressing plants indicate a key role for cytokinin in disease development

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Arabipdosis thaliana (ecotype Col-0) was infected with the root pathogen Plasmodiophora brassicae. Gene expression of the host plant has been analyzed at two time points after inoculation (10 and 23 days after inoculation) compared to the correspondend control plants.

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Plasmodiophora brassicae infection of Arabidopsis thaliana

Arabipdosis thaliana (ecotype Col-0) was infected with the root pathogen Plasmodiophora brassicae. Gene expression of the host plant has been analyzed at two time points after inoculation (10 and 23 days after inoculation) compared to the correspondend control plants.


Affymetrix:Protocol:ExpressionStat

Title: Affymetrix CHP Analysis (ExpressionStat). Description:

Affymetrix:Protocol:Hybridization-EukGE-WS2v4[]

Title: Affymetrix EukGE-WS2v4 Hybridization. Description:

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MEXP-6891

To obtain uniform germination, seeds were moistened and stored for 4 days at 4ºC. Cold treated seeds were placed on the surface of the substrate with the aid of forceps at a distance of approximately 3 cm between seedlings. The substrate, consisting of a 3:1 potting soil:sand mixture, was sieved through a 5 mm mesh and thoroughly moistened. Until germination plant containers were covered with a clear plastic foil to maintain sufficient soil moisture. For the duration of the experiment the soil was moistened by placing plant containers on wetted fleece. For all other experiments plants were grown at same densities (140 plants/box) in flat plastic containers (30 × 47 × 6 cm). Containers were placed in growth cabinets under controlled environment (21 ± 1°C, 16 h light, 100 µmol photons s-1 m-2).

P-MEXP-6893

Soil residue was carefully removed from roots using brushes and the roots were immediately frozen in liquid nitrogen and grounded with mortar and pestle. Total RNA was extracted by the RNeasy Plant Mini kit (Qiagen, The Netherlands) according to the manufacturer’s instructions. RNA samples were further cleaned using Qiagen RNeasy mini-columns 

P-MEXP-6899

labelled according Affymetrix Manual II. 

P-MEXP-6905

Microarray suite 5.0 (Affymetrix) was used for image analysis and to determine probe signal levels. The average intensity of all probe sets was used for normalization and scaled to 100 in the absolute analysis for each probe array. For each microarray, overall intensity normalization for the entire probe sets was performed using Affymetrix Microarray Suite 5.0.

P-MEXP-6907

P-MEXP-7009

For each time point, treatment, and repetition 140 plants were grown and cleaned roots of these plants were pooled in liquid nitrogen before RNA extraction.

P-MEXP-7010

Fourteen day old plants (Boyes key stage 1.04) were inoculated by injecting the soil around each plant with 2 ml of a resting spore suspension of the pathogen Plasmodiophora brassicae (isolate e) with a standard concentration of 10^6 spores/ml.

Plasmodiophora brassicae infection of Arabidopsis thaliana

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