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Additional file 1: Supplementary Figure S1. A histogram comparing the counts of quality-trimmed reads and mapped reads for each biological replicate (Rep1, Rep2, and Rep3) from transgenic (Trans) or wild-type (WT) seedlings at 0-, 6-, and 12-hours post-induction (hpi) or hours post-mock induction (hpmi) as well as the overall mapping rate. I, induced. NI, not induced. Supplementary Figure S2. A principal component analysis (PCA) of the replicates using the read count in the gene-condition count matrix. The PCA shows clustering of replicates and the variance/distance between 6- and 12-h post-induction (hpi) of C4Trans_I replicates and replicates of all other conditions. Trans, transgenic seedlings. WT, wild-type seedlings. I, induced. NI, not induced. Hpmi, hours post-mock induction. Supplementary Figure S3. Co-expression network of DE genes. Differentially expressed genes at 12 h post-induction. Nodes are colored based the node degree of connectivity and edges are colored based on correlation coefficient values. |
