Illumina HiSeq 2500 paired end sequencing; RNA-seq of Pectobacterium carotovorum subsp. carotovorum and P. polaris infecting potato at 24, 48 and 72 hpi, and grown on M9 solid minimal medium at 24 hpi
RNA-seq of Pectobacterium carotovorum subsp. carotovorum and P. polaris infecting potato at 24, 48 and 72 hpi, and grown on M9 solid minimal medium at 24 hpi
Potato minitubers (cv. 'Asterix') were inoculated with bacterial suspension (30 µL, OD600=0.8 in PBS), in vitro control was bacteria on solid M9 minimal medium (70 µL, OD600=0.8 in PBS). Infected potato tissue was harvested at 24, 48 and 72 hpi, and M9 control was harvested at 24 hpi. Samples were frozen in liquid N2 an stored at -80 °C. Macerated potato tissue and bacteria grown on M9 were homogenized in liquid N2 using pestle and mortar. RNA was isolated from the homogenized samples using the Spectrum Plant Total RNA kit (Sigma Aldrich) with the optional on-column DNase digestion (On-Column DNase I Digestion Set, Sigma-Aldrich). Ribosomal RNA was depleted using the RiboMinus Transcriptome Isolation Kit for bacteria (ThermoFisher). Libraries were prepared by the Norwegian Sequencing Centre (NSC). RiboZero ribosome depletion was done before delivery of the samples and NSC performed the remaining library preparation steps using the TruSeq Stranded RNA HT kit (Illumina).