Additional file 4 of Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes
Creators: name: Seyed Rahmani, Razgar
name: Shi, Tao
name: Zhang, Dongzhi
name: Gou, Xiaoping
name: Yi, Jing
name: Miclotte, Giles
name: Marchal, Kathleen
name: Li, Jia
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4: Fig. S1. The T-DNA insertion site for bri1–1D (A), and microscopic images of 7-day old hypocotyl cells for WS2 (B), bri1–5 (C), bri1–5/bak1–1D (D), bri1–5/bri1–1D (E), bri1–5/brs1–1D (F). Fig. S2. PCA plot for assessing the reproducibility of the gene expression dataset. Samples taken from the same genotype are represented in the same color. The plot indicates high consistency between replicate samples as they are located close to each other when plotted on the first and second principal components. Fig. S3. RT-qPCR results for relative expression of selected genes and their corresponding values from microarray analysis. The values represent the log2 of relative expression (sample1/sample2). Rows indicate gene names and columns show the comparison between the indicated lines. Columns with pink header represent the RT-qPCR values, and columns with yellow header are microarray measurements. The red color on the heatmap indicates that the gene has been up-regulated in sample1 as compared to sample2, while blue indicates down-regulation. Fig. S4. Comparing genome-wide expression impact between bri1–5 suppressor lines. Fig. S5. Heatmap of expression of the marker genes that up/down regulation of their expression was confirmed by at least 5 independent references and also affected in the bri1–5 line of our study. For each line, the row-scaled normalized expression data of the 3 biological replicates are shown as adjacent columns. In each row the gradient red color indicates the higher expression for the gene compared to other samples while blue indicates the lower expression. Fig. S6. Pathway analysis (MapMan metabolism) showing for each mutant line the expression changes compared to WS2. Panel A: bri1–5, Panel B: bri1–5/bri1–1D, Panel C: bri1–5/brs1–1D, Panel D: bri1–5/bak1–1D. Fig. S7. Pathway analysis (MapMan: large enzyme families) showing for each mutant line the expression changes compared to WS2. Panel A: bri1–5, Panel B: bri1–5/bri1–1D, Panel C: bri1–5/brs1–1D, Panel D: bri1–5/bak1–1D. Fig. S8. Pathway analysis (MapMan: gene regulation) showing for each mutant line the expression changes compared to WS2. Panel A: bri1–5, Panel B: bri1–5/bri1–1D, Panel C: bri1–5/brs1–1D, Panel D: bri1–5/bak1–1D. Fig. S9. Expression pattern in each mutant line of genes related to ABA signaling, Glutathione metabolism, and ion related hemostasis as discussed in the main text. Mutant lines are represented in the x-axis. The y-axis indicates the log2 normalized expression value of the gene. Table S1. RT-qPCR test of log-fold change (log-FC) of the genes that are overexpressed by activation-tagging in the suppressors at the 7 days seedling stage. Table S2. Summary of the most significant results obtained by MapMan pathway analysis (metabolism, regulation and, large-enzyme families overview). Left column: enriched pathways; entries provide for each line the degree to which the pathway is enriched. P-values are FDR corrected using Benjamini-Hochberg). Table S3. Designed primers for RT-qPCR.