Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem OxBS Illumina microarrays. Supplementary data

Table 1. Multivariable linear regression model outputs for comparing DNA extraction kit performance between BS and oxBS treated samples, with sample source adjusted. Table 2. Linear mixed effect model outputs for comparing DNA extraction kit performance between BS and oxBS treated samples, with sample source included as a random intercept. Table 3. Pairwise Wilcoxon rank sum test p-values from comparing the internal normalization control probe (NORM_A/G/C/T) intensities in BS converted and oxBS converted ccRCC samples. Figure 1. The probe call rate difference across all data sets Figure 2. Principal component regression analysis of technical variables in ccRCC samples Figure 3. Coefficient of variation and ICC in replicate human fetal oligodendrocyte samples. Figure 4. The recommended 5hmC cut-off batch 1 samples batch 2 samples using oxBSQC. Figure 5. The distribution of 5hmC signal in low-quality probe vs high quality probe in batch 1 samples batch 2 samples using oxBSQC. Figure 6. The CpG genomic location enrichment for low-quality probes in batch1 and batch2 using oxBSQC. Figure 7. The distribution of internal normalization control probe (NORM_A/G/C/T) intensities in BS converted and oxBS converted ccRCC samples