IL-25-induced effector-memory ILC2s mediate small intestinal adaptation

This study used bulk ATAC sequencing of epitheilal crypt organoids grown for 6 days, which were isolated from proximal small intestines of wild type mice +50 days after an IL-25 regimen or PBS regimen to study chromatin accessibility. Overall design: Mice (wild type) were injected i.p. with IL-25 (500ng) or PBS 3x a week for 4 weeks and then rested for 50+ days. Epithelial crypts were isolated from the proximal small intestine, grown under standard organoid conditions for 6 days, and organoids isolated from Matrigel and dissociated as detailed below. Cells were washed with basal medium containing 10% FBS, stained in FACS wash buffer containing antibodies for flow cytometry (EpCAM+), then resuspended in FACS wash buffer containing DAPI. Single, live EpCAM+ cells were sorted and 100k cells per sample were used as input for ATAC libraries. Cells were then used for bulk ATAC sequencing.