title: Uninfected 1
design: Phenol-Chloroform: Approximately 0.1 g of stem tissue was collected from the site of inoculation, immediately frozen in liquid nitrogen, and stored at -80C. Another ~0.1 g of tissue was collected from directly below the inoculation site and was ground in bead beater tubes using a PowerLyzer (Qiagen, Hilden, Germany) for two cycles of 2200 rpm for 90 s in each with a 4 min rest between cycles. This material was then dilution plated to measure bacterial colonization. From each biological replicate, we chose six plants with the most similar level of colonization. RNA was extracted from these using a modified hot phenol-chloroform method (DOI: 10.1128/mBio.00114-12). Between 4 and 5 individual plants were pooled per biological replicate. Nucleic acid sample quality was checked using a nanodrop, Agilent bioanalyzer, and qRT-PCR primers Actin_F/R. All samples had RIN values of above 7.2. NEBNext LtraTM Directional RNA Library Prep Kit for Illumina (NEB, Ipswitch, MA, USA) following the manufacturer's recommendation and starting with 3 mg of RNA per sample