Supplementary Figure 10: Global description of DNA methylation data sets.
a, Density histograms of methylation levels (beta values) for Infinium beadarray data sets. Plotted are the density distributions of methylation levels for all examined probes. Each line represents an independent sample. C1–C5: healthy controls; P1, P2: DNMT3AW330R/+ microcephalic dwarfism patients; O1, O2: TBRS overgrowth patients; PCNT1, PCNT2: microcephalic dwarfism patients with PCNT mutation. Bandwidth is defined as the s.d. of the smoothing kernel. b, Median methylation levels (beta values) do not significantly differ between patient and control groups. Each dot represents a sample. Blood samples, n = 2 controls, n = 1 microcephalic dwarfism patient (P2), n = 2 TBRS patients. Fibroblasts, n = 3 controls, n = 2 DNMT3A microcephalic dwarfism patients (P1, P2), n = 2 PCNT microcephalic dwarfism patients. Horizontal bar, mean per group. c, Density histogram of methylation levels for patient 3 and control 3 reduced-representation bisulfite sequencing data sets. Plotted are the density distributions of methylation levels for all CpGs with coverage ≥10. d,e, Genic DNA methylation profiles are similar between patients and controls. Scaled metagene profiles for all autosomal genes plotted (n = 18,754). Each line represents the mean of an individual sample. TSS, transcription start site; TES, transcription end site. f,g, Density histograms of methylation levels for NPC differentiation (f) and mouse cortex (g) reduced-representation bisulfite sequencing data sets. Plotted are the density distributions of methylation levels for all CpGs with coverage ≥10. Each line represents an independent sample. h, Overall methylation level for NPC differentiation and cortex samples from 8-week-old mice in reduced-representation bisulfite sequencing data sets. Plotted is the weighted mean percentage methylation. P value, two-tailed t test. Each dot represents an individual sample. NPCs, n = 3 independent wild-type samples and n = 4 independent W326R samples. Cortexes, n = 3 per group. Horizontal bar, mean per group.
