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. Author manuscript; available in PMC: 2023 Feb 1.
Published in final edited form as: Sci Immunol. 2022 May 13;7(71):eabl6543. doi: 10.1126/sciimmunol.abl6543

Figure 1. Cytokines modify development of small intestinal epithelium in a cytokine-specific manner and correspond to in vivo infection models.

Figure 1

A, Image segmentation and classification of organoid images. B, Bright field images of small intestinal organoids treated with 10 ng/mL cytokine since the day of splitting. Images are projection of Z-stack. C, Distribution of gray value (higher value is whiter) and area of all organoids in same experiment as B. Percentages are relative to total number of organoids in that treatment. Plot shows distribution of in total 2,310 organoids, representative result of 5 mice. D, Time points for RNAseq experiment from small intestinal organoids treated with 10 ng/mL cytokine. E, PCA plot of log2(TPM + 1) values determined with RNAseq as shown in D. Each circle is one biological replicate. F, Number of up-regulated significant genes from same RNAseq experiment as in D (p<0.05 and log2fc>1). G, GSEA using genesets consisting of the 300 most significantly up-regulated genes from intestinal epithelium from mice infected with N. brasiliensis or C. rodentium. These genesets are compared to RNAseq of intestinal organoids stimulated with indicated cytokine compared to control. See supplementary file 1 for genesets. NES = normalised enrichment score.