Overview of differentially expressed genes for <i>SbCCoAOMT-</i>9a (9a) and <i>SbCCoAOMT</i>-28b (28b) in leaf and stalk tissue compared to wild-type.

Principal components analysis of RNA-seq data on individual samples from wild-type and SbCCoAOMT in (A) leaf and (B) stalk tissue. Venn diagrams of (C) increased and (D) decreased genes detected in RNA-seq experiments. (E) Heatmap analysis of differentially expressed genes in leaves (L) and stalks (S) for wild-type (WT), SbCCoAOMT-9a (9a) and SbCCoAOMT-28b (28b). Differentially expressed genes were determined using DESeq2 with a threshold of FDR 1.0. Numbers within regions in venn diagram indicate common and unique genes within each sector. Raw counts of genes that were differentially expressed in at least one 35::SbCCoAOMT line relative to wild-type were log-transformed and Z-score standardized for a normalized expression value. Heatmap was prepared using hierarchial clustering analysis in JMP 12.2.0 (SAS Institute Inc.). Letters (A-G) within heatmap indicate hierarchial clusters of genes.