Extended Data Fig. 4: DNA methylation heterogeneity in ILCP2s.
a-c, Representative flow cytometry plots showing expression of UHRF1-mCherry in Lin(CD3/CD19/CD11b/Gr-1/TER-119/CD45R)−CD45+CD127+NK1.1+NKp46+ ILC1s (a), Lin(CD3/CD19/CD11b/Gr-1/TER-119/CD45R)−CD45+CD127+KLRG1+ ILC2s (b) and Lin(CD3/CD19/CD11b/Gr-1/TER-119/CD45R/NK1.1/KLRG1)−CD45loCD127+CD90hi ILC3s (c) from the small intestine of UHRF1-mCherry reporter mice and WT mice. d, tSNE plot showing gene expression analysis of ILCP1s, ILCP2s, mCherry+ ILCPs, mCherry− ILCPs, and mCherry+ ILCPs cultured in vitro for two days (Day 2 in vitro). e, Heatmap showing the expression of marker genes of ILCP1s and ILCP2s in ILCP1s, ILCP2s, mCherry+ ILCPs, mCherry− ILCPs, and mCherry+ ILCPs cultured in vitro for two days. f, Heatmap showing WCG methylation levels of selected SMRs in ILCP1s (n = 106 cells), ILCP2_ILC1s (n = 67 cells), ILCP2_ILC2s (n = 69 cells), and ILCP2_ILC3s (n = 70 cells). g, Dot plot showing RNA expression levels of SMR-related genes, including ILCP signature genes (Zbtb16 and Tox), ILC1 signature genes (Tbx21 and Ifng), ILC2 signature genes (Bcl11b and Il4), and ILC3 signature genes (Rorc and Il17a) in ILCP2_ILC1, ILCP2_ILC2, ILCP2_ILC3, ILC1, ILC2 and ILC3 subsets. h, Dot plot displaying GCH methylation levels at SMRs in ILCP and ILC signature genes in ILCP2_ILC1, ILCP2_ILC2, ILCP2_ILC3, ILC1, ILC2 and ILC3 subsets. i, UMAP analysis showing cell type clustering based on transcriptome data of ILCP2_ILC1s (n = 67 cells), ILCP2_ILC2s (n = 69 cells), ILCP2_ILC3s (n = 70 cells), ILC1Ps (n = 46 cells), ILC2Ps (n = 43 cells), and ILC3Ps (n = 35 cells). (ILC1Ps, ILC2Ps, and ILC3Ps from dataset GSE131038 and GSE193835). j, Heatmap showing expression levels of representative ILC marker genes in ILCP2 subsets and precursor cells of ILCs. Lineage-determining transcription factors are highlighted in red. Statistical analyses were performed using two-sided Wilcoxon rank sum test. Data represented at least two (d-j) or three (a-c) independent experiments.
