Fig. 5: Spatial-DMT resolves mitotic history and subtle region-specific epigenetic variations.

a, Differential region analysis between adjacent WNN cell clusters (left). Chromatin features enriched at hypomethylated genome loci in the blue region (middle) and those enriched in the red region (right) are shown. A summary of the ChromHMMfullStack (full-stack chromatin hidden Markov model) annotation is provided in Supplementary Table 6. HM, histone modification; TFBSrm, transcription factor binding sites from roadmap dataset. b, Differential region analysis in the same WNN (W7) cell cluster but across spatially distant locations (left). Chromatin features enriched at hypomethylated loci in the blue (middle) and red (right) regions are shown. False discovery rate (FDR) from one-sided Fisher’s exact test. c–e, Methylation levels at PMDs in the E11 mouse embryo (c), E13 mouse embryo (d) and P21 mouse brain (e). f, Enriched TF motifs from Homer one-sided hypergeometric test q value (on the basis of Benjamini–Hochberg procedure) in differentially hypomethylated VMRs between D0 and D4 cluster pixels derived from cluster R3 in the E11 embryo (two-sided Wilcoxon rank-sum test, adjusted P value on the basis of Bonferroni correction). g, Differentially expressed genes corresponding to the D0 and D4 pixels originated from the R3 cluster in the E11 embryo (Wilcoxon rank-sum test (two-sided), adjusted P value on the basis of Bonferroni correction).