Extended Data Figure 4: Controls and annotation of methylation pattern clusters.

a, Propidium iodide intensity distribution of H9 human ES cells, illustrating the S and G phase gating we used in order to compare methylation distributions along the cell cycle. b, UMI-bis was performed on H9 human ES cells and WI38 cells that were sorted into G1 and S populations. Shown is average methylation for well covered fragments in the two data sets. This analysis confirms that the heterogeneity we observe in the methylation patterns is not linked directly to cell-cycle effects. c, Annotation of the pattern clusters in the high and intermediate methylation classes, as shown in Fig. 2. The different classes are not strongly linked to transcription start sites (TSSs), exons or H3K27me3 occupancy. d, Cancer cell line methylation distributions for loci classified according to the WI38 pattern clusters. e, Distributions of lamina association and time of replication (Imr90 Repli-Seq data) for loci associated with the different pattern clusters discussed in Figs 1 and 2.