Extended Data Fig. 4: Further analysis of DNA methylation data quality of Spatial-DMT.

a, Genomic uniformity analysis showing the fold enrichment (observed overlaps divided by expected overlaps) for different genomic features, comparing E11, E13 embryos, and P21 brain samples with reference datasets^{5,10,12,14,16} (n = 32 cells for 2021_Shareef, n = 103560 cells for 2021_Liu, n = 107 samples for 2020_He, n = 491 cells for 2022_Nichols_mm10, n = 260 cells for 2019_Hernando, n = 2,493 for E11 embryo (10 μm), n = 1,954 for E11 embryo 1 (50 μm), n = 1,947 for E11 embryo 2 (50 μm), n = 1,699 for E13 embryo (50 μm), and n = 2,235 for P21 brain (20 μm), same for b). b, DNA methylation levels under different chromatin states, comparing E11, E13 embryos, and P21 brain samples with reference datasets^{5,10,12,14,16}. The y-axis represents the methylation levels, with different chromatin states on the x-axis. These chromatin states include active states such as active transcription start site (TSS)-proximal promoter states (TssFlink), actively-transcribed states (Tx, TxWk), enhancer states (Enh, EnhG, EnhLo, EnhPois, EnhPr). Inactive states consist of constitutive heterochromatin (Het), quiescent states (Quies, Quies3, Quies4, QuiesG), repressed Polycomb states (ReprPC, ReprPCWk), and bivalent regulatory states (TssBiv). Boxplots in a and b contain the central line, which represents the median, the lower and upper hinges indicate the first and third quartiles, and the whiskers extend to the most extreme data points within 1.5 times the interquartile range (IQR) from the hinges. c, Line plots showing the mean DNA methylation levels (%) across different genomic regions for E11, E13 embryos, and P21 brain samples. The x-axis represents the genomic regions, and the y-axis represents the mean methylation levels. Error bands represent mean values ± 1 standard deviation. d, Histogram and pie chart showing the size distribution and genomic annotation of variably methylated regions (VMRs) identified in the E11 embryo. The pie chart indicates the percentage of VMRs in different genomic features, such as promoters, exons, and intergenic regions. e, Confusion matrix illustrating the correspondence between clustering results derived from RNA transcription and DNA methylation data in the E11 embryo. f, Alluvial diagram showing the relationships among clusters identified by DNA methylation, RNA, and WNN integration in the E11 embryo. g, Modality weights indicating the relative contributions of gene expression and DNA methylation for each WNN cluster in the E11 embryo.