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