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. 2023 Sep 30;14:6109. doi: 10.1038/s41467-023-41683-y

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© The Author(s) 2023, corrected publication 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — a Experimental scheme of IFNγ treatment of intestinal organoids. b Brightfield images of intestinal organoids that were treated with different concentration of IFNγ for 5 days. Non-treated cultures served as control. Apoptotic cells are indicated by arrow. Scale bar 200 µm. c–f Time-course analysis of organoids stimulated with different concentration of IFNγ for 5 days. Dissociated organoid cells were analyzed by FACS after cKit, MHCII, and DAPI staining. c viable cell percentage, d Lgr5⁺ cell percentage, e MHCII⁺ cell percentage, and f cKit⁺ cell percentage. Each dot represents one mouse. n = 9 mice per group were analyzed. Error bars represent the SD. P value was calculated by two-sided Welch’s t test. g UMAP projection of organoid culture derived EpCAM⁺ cells presenting seven different clusters, clustered via shared nearest neighbor modularity optimization-based clustering algorithm. Clusters were identified to epithelial cell types by using expressed markers. n $\geq$ 3 mice per group were analyzed. h Bar chart of odds ratio with 95% confidence interval showing the relative abundance of different epithelial cells changing after IFNγ treatment. P value was calculated by two-sided hypergeometric test. i, j Boxplots of geneset enrichment analyses of the indicated gene datasets in the in vitro treated intestinal organoids treated with 2 ng/ml IFNγ for 24 h. P value was calculated by two-sided Wilcoxon non-paired test. k The bar charts show the percentage of Ccl5⁺ CD4 Cytotoxic T cells (left panel) and Klrg1⁺ ILC2s (right panel) in the indicated conditions. Organoids were derived from old mice. n = 4 mice per group were analyzed. Error bars represent the SD. P value was calculated by two-sided Welch’s t test. l The bar charts show the percentage of Ccl5⁺ CD4 Cytotoxic T cells (left panel) and Klrg1⁺ ILC2s (right panel) in the indicated conditions. Organoids were derived from young mice. n = 4 mice per group were analyzed. Error bars represent the SD. P value was calculated by two-sided Welch’s t test.