Pathogen invasion in plants is associated with transcriptional reprogramming. Enigmatically, plants induce similar transcriptome responses upon infection by virulent or avirulent pathogens. This renders the importance of transcriptional reprogramming for immunity obscure. Here, using RNA-seq, we generate time-series transcriptome data coupled with genetic perturbations to reveal temporal dynamics upon infection by virulent or avirulent strains of a bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana. Fast and sustained transcriptional reprogramming occurs upon infection with avirulent strains while virulent strain infection leads to a slower response with comparable gene expression patterns and magnitudes. Importantly, transcriptome analysis of resistant and susceptible mutants responding to avirulent strains links delayed transcriptional reprogramming to compromised immunity. Taken together, our results pinpoint the early critical time window of transcriptional reprogramming for establishing effective immunity against the bacterial pathogen. Overall design: Leaves of Col-0 and all the single, double, triple and quadruple mutants of dde2-2, ein2-1, pad4-1, sid2-2 were syringe-infiltrated with mock (water) or suspensions of Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) carrying an empty vector (pLAFR), Pto DC3000 carrying AvrRpt2, or Pto DC3000 carrying AvrRpm1 at the OD600 of 0.001. Similarly, leaves of the rpm1-3 rps2-101C mutant plants were inoculated with mock, Pto DC3000 carrying AvrRpt2 or Pto DC3000 carrying AvrRpm1. Three fully-expanded leaves (leaves 7-9) from three different plants were harvested as a single biological replicate at 1, 2, 3, 4, 6, 9, 12, 16, 20, 24, 36, 48 hours post inoculation (hpi). To generate three biological replicates, three independent experimental trials were carried out, in which plant positions within pots and growth chambers were randomized in order to avoid undesirable systematic effects. For the statistcal analysis, 348 samples (M001-M348) were used.