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Cultivated potato is the world’s number one non-grain food commodity. The late blight pathogen <i>Phytophthora infestans</i> has the capacity to attack both potato foliage and tubers. Importantly, foliar resistance against late blight does not guarantee tuber resistance, contrasting phenotypes can happen even within the same genotype. Most potato transcriptome studies targeted foliage and few studies target tuber-microbe interactions. We conducted a time-course RNA-seq study consisting of two genotypes (wild type susceptible and transgenic resistant lines), two treatments (with and without <i>P. infestans</i>), three time points, and three bio-reps for both tuber and foliage samples (72 samples in total, 36 for tubers, 36 for foliage). Around one billion paired-end Illumina Hi-Seq reads were generated; the majority of them were mapped uniquely to one location in the reference genome. We analyzed the transcription levels of over 30,000 potato genes using various software packages. We discovered marked transcriptome differences among genotypes and organs (tuber and foliage). Various regulatory and metabolic pathways were identified to distinguish transgene and organ specific defense responses.<p><p>Keywords: Oomycete, Root-Tuber Crops, Potato