RNA-seq of VIGS tomato
Total RNA was extracted from TRV2 control and TRV2-SlTAGL1 tomato pericarp samples using an RNeasy MiniKit (QIAGEN). RNA degradation and contamination was checked on 1% agarose gels. RNA purity was monitored using NanoPhotometer spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturers and index codes were added to attribute sequences to each sample. Library quality was assessed on Aglient Bioanalyzer 2100 system. According to the manufacturers instructions, the clustering of the index-coded samples was performed on a cBot Cluster Generation System using Hiseq 4000 PE Cluster Kit (Illumia). After cluster generation, the library preparation were sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.