Intestinal tissue was fixed, processed and haematoxylin and eosin stained as described previously [41 (link)]. The following antibodies were used for immunohistochemistry: anti-Cd4(1:100; eBioscience), anti-Cd8 (1:200; eBioscience) anti-Caspase 3 (1:750; R&D systems), anti-β-catenin (1/50; Becton Dickinson), anti-Ki67 (1:200; Vector Labs) and mouse anti-BrdU (1:100; Becton Dickinson). Staining for Treg cells was performed on a Ventana (Roche) Discovery Ultra Autostainer (Serial number 313108) using Antigen Retrieval CC1 buffer (Ventana) for 48 minutes at 95° C and an Anti-mouse/rat FoxP3 (1/25; eBioscience) in discovery antibody diluent (Roche).
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