For the microarray experiments to compare the gene expression profiles of ate1 ate2 and wild-type seedlings, 11-day-old whole seedlings of the double mutant and of the wild type Col-0 were grown at 22 °C under long-day conditions (16 h light/8 h darkness) on 0.5xMS agar medium. Tissue from ~40 seedlings per genotype was used for RNA extraction. In total, six biologically independent sets of samples were generated.
For the transcriptomics experiment carried out to monitor the response of ate1 ate2 and wild-type Col-0 plants to Pst AvrRpm1, 4-week-old plants (grown in a completely randomized experimental design) were inoculated with Pst AvrRpm1 (5 × 107 cfu/mL) or mock-inoculated (10 mM MgCl2). Leaves were collected immediately after infiltration (t0), at 2 and at 4 h after inoculation. In total, four biological replicates were generated with four plants per genotype (four inoculated leaves per plant).
For both transcriptomics experiments (i.e. seedlings and response to Pst AvrRpm1), total RNA was isolated from plant tissue using the Spectrum Plant total RNA kit (Sigma), and was co-hybridized to custom-designed microarrays (Agilent) as previously described in Kaufmann et al.56 (link).
For the transcriptomics experiment carried out to monitor the response of ate1 ate2 and wild-type Col-0 plants to Pst AvrRpm1, 4-week-old plants (grown in a completely randomized experimental design) were inoculated with Pst AvrRpm1 (5 × 107 cfu/mL) or mock-inoculated (10 mM MgCl2). Leaves were collected immediately after infiltration (t0), at 2 and at 4 h after inoculation. In total, four biological replicates were generated with four plants per genotype (four inoculated leaves per plant).
For both transcriptomics experiments (i.e. seedlings and response to Pst AvrRpm1), total RNA was isolated from plant tissue using the Spectrum Plant total RNA kit (Sigma), and was co-hybridized to custom-designed microarrays (Agilent) as previously described in Kaufmann et al.56 (link).