Figure 2. IL-13 and IL-22 induce different subsets of goblet cell genes.

A, Heatmap of NES values from GSEA analysis of gene sets representing different cell types compared to RNAseq data from organoids treated for 24 hours with cytokines, see supplementary file 1 for gene sets. B, Distribution of how the goblet cell gene set from plate based scRNAseq from Haber et al is changed upon 24 hour IL-13 and IL-22 treatment in organoids. Up is defined as log2fc>0.5 and p-adj<0.05. C, Gene expression from intestinal organoids treated for 24 hours with indicated cytokine. Statistics calculated with DESeq2, details in methods. D, E, Confocal staining of MUC2 and UEA1 2 days after splitting (D) and RELMβ and UEA1 at 3 days after splitting (E) in small intestinal organoids. Representative images of three mice. 5 ng/mL of IL-22 and 10 ng/mL of IL-13 was used. F,G, Quantification of images acquired as in D and E. Pixels are defined as positive above a set threshold. Each circle represents one organoid and statistics calculated with unpaired two tailed T-test. H, See C. I, GSEA of IL-22 specific goblet cell genes from B compared to RNAseq data from organoids stimulated with IL-22 for 1h and 4h. All images are projections of Z-stacks.