RNA-Seq_XpAL65_Tomato_Apoplast_24hr_Rep_3
Apoplastic populations of XpAL65 were established by vacuum infiltrating tomato leaves with bacterial suspensions. Inoculum densities of 10 CFU/ml for the 24 h time point was used to ensure sufficient cell recovery. Plants were incubated in the greenhouse and sampled at 24 hours post-inoculation. For each time point, 80100 leaves were processed in RNA-stabilizing solution, sonicated, filtered, and centrifuged to isolate bacterial cells, followed by multiple washing and filtration steps to remove plant debris. Cell pellets were flash frozen and stored at 20 C. Each time point consisted of three biological replicates, each derived from 80100 leaves. RNA was extracted using Trizol method. Samples were DNAse treated with Invitrogen DNAse (RNAse free). Library preparation was performed using Illuminas Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices. Sequencing was done on a NovaSeq X Plus, producing paired end 150bp reads. Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4)