Extended Data Fig. 2: Chromatin accessibility and DNA methylation properties of ILCP1s and ILCP2s.

a, GCH methylation analysis showing chromatin accessibility 1 kb upstream and 1 kb downstream of the transcription start sites (TSSs) in ILCP1s and ILCP2s. b, GCH methylation analysis showing chromatin accessibility around 2 kb upstream and 2 kb downstream of the gene body in ILCP1s and ILCP2s. c, Bar plot showing relative enrichment scores of NDRs in genomic elements in ILCP subsets. Enrichment scores were calculated as the ratio of NDRs in each genomic element compared to genomic background. SINE (short interspersed nuclear element), LINE (long interspersed nuclear element), LTR (long terminal repeat). d, Heatmap showing chromatin accessibility of common NDRs (C1, n = 16,898), ILCP1-specific NDRs (C2, n = 23,021), and ILCP2-specific NDRs (C3, n = 56,986) in ILCP1s and ILCP2s. e, Pie charts showing distribution of common NDRs (C1), ILCP1-specific NDRs (C2), and ILCP2-specific NDRs (C3) across genomic elements in ILCP1s and ILCP2s. f, Alluvial plots showing dynamic changes of promoter states (homogeneously open, divergent, closed) from ILCP1s to ILCP2s. g, Bar graph showing the distribution of DNA methylation levels in all WCG sites in ILCP1s and ILCP2s. All DNA methylation values were retained to one decimal place. h, Boxplot showing the expression levels of Dnmt1 and Uhrf1 genes in ILCP1s (n = 106 cells) and ILCP2s (n = 206 cells). Each box represented the median and the 25% and 75% quartiles, and the whiskers indicate 1.5 times the interquartile range. Statistical analyses were performed using two-tailed unpaired Student’s t test. i, Two-dimensional plot showing the dynamic expression of scores for DNA methylation maintenance genes along the pseudotime. Data are representative of at least two independent experiments.