Supplementary Figures 1-8, Supplementary Tables 1-3 from Identification of DNA Methylation–Independent Epigenetic Events Underlying Clear Cell Renal Cell Carcinoma

Supplementary Figure 1. Quantitation and location of epigenetic changes in all 6 patient samples. Supplementary Figure 2. Significant accessibility changes between 6 patients. Supplementary Figure 3. Accessibility changes shared in at least two patient samples, plotted in heatmaps, either losing accessibility (Groups a and e) or gaining accessibility (Groups d and f) with or without DNA methylation. Supplementary Figure 4. ChIP-seq analyses of Patient 5. Supplementary Figure 5. Validation of AcceSssIble data from each Group a, d, e, and f using locus-specific bisulfite sequencing. Supplementary Figure 6. Correlation plots of chromatin accessibility and DNA methylation changes vs. gene expression changes. Supplementary Figure 7. Epigenetically-regulated genes in the HIF1A-signaling pathway and VHL status in each ccRCC patient. Supplementary Figure 8. Example diagram of M.SssI treatment efficacy. Supplementary Table 1. List of loci with methylation-dependent accessibility changes that positively correlate with expression changes from TCGA RNA-seq data. Supplementary Table 2. List of loci with methylation-independent accessibility changes that positively correlate with expression changes from TCGA RNA-seq data. Supplementary Table 3. List of genes overlapping between epigenetically-regulated genes from our study, and commonly mutated genes in ccRCC from TCGA.