Hiseq2000 100pe

Infiltrated leaf tissue was harvested 3 days post infiltration. Total RNA was extracted from the infiltrated leaf tissue using RNeasy Plant Mini Kit (Qiagen). RNAseq libraries were prepared from the triplicate samples for each type of infiltration, using 500 ng of total RNA, and indexed with the TruSeq mRNA Library Prep Kit according to the protocol (Illumina). The same amount of each RNAseq library was pooled and run on one lane of HiSeq2000 100PE (Illumina).
The quality of the sequencing reads was assessed with FASTQC [60 ]. RNA sequencing reads were trimmed using DynamicTrim (Phred score ≥20) and filtered on length (≥ 25 bp) using LengthSort [63 (link)]. RNAseq reads were aligned against the N. benthamiana transcriptome [64 (link)] using Bowtie2 v2.1.0 [65 (link)], and RSEM v1.2.3 [66 ] generated raw read counts for each transcript. DESeq [67 (link)] was used to run three differential expression analysis tests: (1) between Buffer infiltrated and Agrobacterium infiltrated; (2) between Agrobacterium and Agrobacterium containing AcMYB10; (3) between Agrobacterium and Agrobacterium containing AtLEC2. Lists of differentially expressed transcripts with a FDR adjusted P value <0.001 are shown in Additional file 7: Table S5, Additional file 8: Table S6, and Additional file 9: Table S7, respectively.