Transcriptional dynamics driving MAMP-triggered immunity and pathogen effector-mediated immunosuppression in Arabidopsis leaves following infection with Pseudomonas syringae pv. tomato DC3000.. Arabidopsis thaliana

High-resolution temporal transcriptomic analysis of Arabidopsis thaliana leaves during infection by Pseudomonas syringae DC3000 and DC3000hrpA-thaliana Overall design: RNA was extracted from Arabidopsis leaves after mock-inoculation, infection with P. syringae DC3000 and infection with P. syringae DC3000hrpA-. 13 time points (0, 2, 3, 4, 6, 7, 8, 10, 11, 12, 14, 16, 17.5 hours post inoculation) were sampled from each treatment and four biological replicates (a single leaf) were harvested at each time point for each treatment. This led to 156 biological samples (13 time points x 3 treatments x 4 biological replicates). Four technical replicates of each biological sample were generated (624). The microarrays were two-channel CATMA arrays and hence two samples are hybridized to each array resulting in 312 arrays used in the experiment. A “loop design” was developed to enable efficient extraction of information about sample comparisons. Half the arrays were used to directly compare samples at different time points within the same treatment, and half directly compared the same time point and adjacent time points between treatments. This design maximizes the power of data comparisons over time and between treatments.