Extended Data Fig. 1: Gating of immune cells from the large intestine of mice.

a. Cells were isolated from the large intestine lamina propria of RORγt^EGFP reporter mice. Two populations, TCRβ⁺ cells and TCRβ⁻ cells, of RORγt⁺ immune cells were sorted separately and equally mixed at a 1:1 ratio, permitting enrichment of non-T lymphocytes populations. b. Gating strategy for different immune cells with surface markers. Lineage markers included: CD3, CD5, NK1.1, TCRγδ, Ly6G. B cells were gated as CD45⁺CD19⁺; Macrophages (Mac) were gated as CD45⁺CD64⁺MHCII⁺; cDCs were gated as CD45⁺Lin⁻CD64⁻CD11^hiMHCII^hi. CD4⁺ T cells were gated as CD45⁺Lin⁺CD4⁺; ILC2s were gated as CD45⁺Lin⁻CD64⁻CD11c⁻CD127⁺CD90⁺KLRG1⁺; ILC3s were gated as CD45^dimLin⁻CD64⁻CD11c⁻CD127⁺CD90^hiKLRG1⁻; ILC3s were further gated as CCR6⁺, NKp46⁺ or DN subset. c. Gating strategy for different immune cells with transcription factors. Lineage 1: CD3, CD5, NK1.1, TCRγδ, Ly6G. Lineage 2: F4/80 and B220. cDCs were gated as CD45⁺Lin⁻CD11^hiMHCII^hi; T_H17 cells were gated as CD45⁺Lin⁺CD4⁺FoxP3⁻RORγt⁺; ILC3s were gated as CD45⁺Lin⁻CD11c⁻CD127⁺CD90⁺RORγt⁺, and further gated as CCR6⁺, T-bet⁺, or DN; ILC2s were gated as CD45⁺Lin⁻CD11c⁻CD127⁺CD90⁺RORγt⁻T-bet⁻.