Extended Data Fig. 4: Flow cytometry gating for ILCs and CTLA-4.

a, Gating strategy for flow cytometry analysis of different immune cells in intestinal lamina propria of mice. Lineage 1, CD11b, CD11c, F4/80 and B220; lineage 2, CD3ε, CD5, CD8α and TCRγδ; Group 1 innate lymphoid cells (ILC1s) were identified as live CD45⁺ Lineage⁻ CD127⁺ CD90.2⁺ T-bet⁺ RORγ⁻ NK1.1⁺ Eomes⁻; group 2 innate lymphoid cells (ILC2s) were identified as live CD45⁺ Lineage⁻ CD127⁺ CD90.2⁺ GATA3⁺; group 3 innate lymphoid cells (ILC3s) were identified as live CD45⁺ Lineage⁻ CD127⁺ CD90.2⁺ RORγ⁺; and subsets of ILC3s were further identified as CCR6⁺ T-bet⁻ ILC3s or CCR6⁻ T-bet⁺ ILC3s. For T cell analysis Tregs were identified as CD45⁺CD4⁺FoxP3⁺ T cells and T_H 17 as CD45⁺CD4⁺ RORγ⁺FoxP3⁻ T cells. b, Representative flow cytometry plots of CTLA-4 staining in different immune cells from small intestine lamina propria of C57BL/6 mice (n = 4 mice). c, Flow cytometry plots of CTLA-4⁺ cells in small intestine lamina propria of Rag1^−/− mice (n = 4 mice). Data in b and c are representative of two independent experiments with similar results.