Expression data from elicitor-treated Arabidopsis seedling roots [25min]

Plants can perceive the presence of pathogens at the cell surface and plant damage-derived molecules via recognition of conserved microbial molecules, named pathogen- or microbe-associated molecular patterns (PAMPs) and damage associated molecular patterns (DAMPs). Well-studied examples of PAMPs are chito-oligomers, breakdown products of fungal cell walls and insect exoskeletons. Pectin-derived oligogalacturonides (OGs) are well-characterized DAMPs. Both PAMPs nd DAMPs are capable of activating plant immunity, generating changes in gene expression that lead to increased production of defense compounds and proteins; thus, equipping the plant cell to defend itself. We used microarrays to assess the gene expression changes that follow 25min after elicitor treatment. RNA was extracted from roots of seedlings treated with cellobiose, chito-oligomers, OGs or a no-elicitor control, for 25 min using Trizol LS (Invitrogen) according to the manufacturer's recommendations. RNA integrity was checked with an Agilent 2100 BioAnalyzer. An aliquot from each RNA sample was used as a template to make cDNA, which was assessed by qRT-PCR to confirm that samples had the expected WRKY30 expression profile at 25 min. Samples were then analyzed for gene expression with Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays, using standard Affymetrix reagents and protocols at the QB3-Functional Genomics Lab at the University of California, Berkeley. Samples from three biological replicas for each treatment were analyzed. A total of 24 chips were used (4 treatments x 2 time points x 3 biological replicates). Microarray data were analyzed using the GCRMA algorithm as described previously (Fletcher et al., 2011); ratios of normalized probe set intensity values were calculated for each sample pair (in which M value = log2 [elicitor/control]) and then averaged among the three replicates.