Transcription profiling by array of Arabidopsis mutant for npr1 after treatment with 3,5-dichloroanthranilic acid or 2,6-dichloroisonicotinic acid

DCA (3,5-Dichloroanthranilic acid) is a newly identified synthetic defense elicitor. To perform a comparative analysis of defense responses triggered by DCA and the structurally related defense inducer INA (2,6-Dichloroisonicotinic acid) Affymetrix chip experiments were performed with Arabidopsis thaliana seedlings treated with one of these two compounds. Experiment Overall Design: Arabidopsis thaliana plants (accession Col-0) were grown on soil in a semi-sterile growth chamber under fluorescent lights (14 hours light, 10 hours dark, 21 centi grades, 100 Einstein/m2/s). Wild type Col-0 plants and the npr1-3 mutant were used in this study. Aerial tissues of 2 week old soil grown Arabidopsis seedlings were sprayed with 100uM 3,5-Dichloroanthranilic acid (DCA), or 100uM 2,6-Dichloroisonicotinic acid (INA) or mock solution and harvested 48h or 6 days after the treatment. Final DMSO concentrations never exceeded 0.002%. Mock treatments were application of 0.002% DMSO in water. For harvesting the aerial plant parts were shock-frozen in liquid nitrogen. Total RNA was isolated from seedlings using TRIZOL (Invitrogen) follwing the manufacturer’s instructions. RNA was processed and hybridized to Affymetrix Arabidopsis ATH1 genome array GeneChip following manufacturer’s instructions (Affymetrix) by the University of California, Riverside Core Instrument Facility. Three independent biological replicates were performed for each treatment.