Extended Data Fig. 6: H3K27me3 scEpi²-seq for on mouse intestinal samples.

a. CellTrace labeling and visualization of intestinal fractions by flow cytometry. b. log₂ fold changes of H3K27me3 signal on genes (each dot indicates a gene, color indicates adj. P-value, default likelihood ratio test using Signac) from 3 individual mice split by Absorptive, Secretory and Immune cells (x-axis, coarse Signac clusters, see Methods). Each facet contains genes associated with either Absorptive, Secretory or Immune cells (Supplementary Table 4). The boxplot is defined by the median ± interquartile range (IQR) and whiskers represent 1.5× IQR c. Heatmap with histone modification signal intensities (no. of ChIC counts) of single intestinal cells (rows) split by coarse Signac clusters (that is, Absorptive, Secretory and Immune) for a representative region on chromosome 1. d. Average CpG methylation (y-axis) in relation to distance from the cut site (x-axis). e. Single-cell heatmap for cut site spacing in intestinal cells split by coarse Signac cluster (that is, Absorptive, Secretory and Immune). The read pair correlation shows characteristic oscillations related to nucleosome spacing. f. Coverage plot of normalized H3K27me3 signal between Enteroendocrine cells and Goblet cells for a region containing the Gfi1 gene (expressed in Goblet cells). g. Coverage plot of normalized H3K27me3 signal between Enteroendocrine cells and Goblet cells for a region containing the Pax6 gene (expressed in EECs). h. Coverage plot of normalized H3K27me3 signal between T-cells, B-cells and Myeloid cells for a region containing the Lyn gene (expressed in B-cell and Myeloid cells). i. Coverage plot of normalized H3K27me3 signal between T-cells, B-cells and Myeloid cells for a region containing the Il10ra gene (expressed in B-cells and T-cells). j. Coverage plot of normalized H3K27me3 signal between T-cells, B-cells and Myeloid cells for a region containing the Syk gene (expressed in B-cells and Myeloid cells). k. Coverage of CpG per single cell (y-axis) versus average CpG methylation (x-axis) per single cell (each dot). Each dot is colored by quality control (pass/fail), cells that pass QC were used for downstream analysis. l. UMAPs generated from CpG methylation using MethSCAn. Cells are colored based on two 5mC clusters retrieved from Leiden clustering on the residuals on the variable methylated regions (see Methods). m. Fraction of 5mC cluster (y-axis) derived from Leiden clustering over the three individual mice (x-axis). n. Difference in CpG methylation (x-axis) and adj. P-value, y-axis) for each identified Differentially Methylated Regions (DMRs) by MethSCAn between 5mC cluster pseudobulks and all pairwise combination between pseudo-bulks from all H3K27me3 subclusters. Dots are colored by significant and non-significant DMRs derived using a two-sided t-test (CpG coverage pseudobulk > 25 within DMR an adj. P-value < 0.001).