Extended Data Fig. 1: Single-cell multi-omics analyses reveal two developmental stages of ILCPs.

a, Schematic representation showing the isolation of Lin(CD3/CD19/CD11b/Gr-1/TER-119/CD45R)⁻CD45⁺CD127⁺NK1.1⁺NKp46⁺ ILC1s and Lin(CD3/CD19/CD11b/Gr-1/TER-119/CD45R)⁻CD45⁺CD127⁺KLRG1⁺ ILC2s from the lamina propria of small intestine of wild-type (WT) C57BL/6 mice and Lin(CD3/CD19/CD11b/Gr-1/TER-119/CD45R/NK1.1/KLRG1)⁻CD45⁺CD127⁺RORγt-GFP⁺ ILC3s from RORγt-GFP⁺ mice, Lin(CD3/CD19/CD45R/CD11b/TER-119/Gr-1)⁻c-Kit⁺CD127⁺α4β7⁺PLZF-GFP⁺ ILCPs from the bone marrow of Zbtb16 (encodes PLZF)-GFP mice, followed by single-cell multi-omics sequencing and analyses of the transcriptome, chromatin accessibility and DNA methylome. b, Flow cytometry gating strategy showing the isolation of Lin(CD3/CD19/CD45R/CD11b/TER-119/Gr-1)⁻CD127⁺c-Kit⁺α4β7⁺PLZF-GFP⁺ ILCPs from bone marrow of Zbtb16-GFP mice. c, Heatmap showing expression levels of the marker genes in ILCP1s and ILCP2s. Statistical analyses were performed using Wilcoxon Rank Sum test. d, UMAP plots showing the distribution of CytoTRACE scores in ILCPs. e, RNA velocity analysis showing potential developmental trajectories of ILCPs. f, Dot plot showing positive regulation of lymphoid differentiation scores along pseudotime in ILCPs, calculated using the AddModuleScore function. g, Two-dimensional plots showing dynamic expression of Dnmt1 and Uhrf1 genes in ILCPs along the pseudotime. b-g, Data are representative of at least two independent experiments. Schematic in a was created using BioRender.com.