Extended Data Fig. 9: Expression of cytokines and chemokine for eTreg function.

a. Co-occurrence analysis of Hh (left top) and Hh/anti-IL-10R (left bottom) with the ratio of the two conditions (right). Size of dots represents p-values and the colour represents fold change. Number of spots analysed after removing Muscularis-associated NMF factors (4405 spots) are Hh/anti-IL-10R: 9572 spots and Hh: 8815 spots. b. Chord diagrams showing significant interactions of Tregs with lymphoid and myeloid cells in LP (top) and LA (bottom). Restricted to cell types with >30 cells per region and significance p < 0.05 for interactions between any cell pair. c.Dot plot showing relative expression by NICHE-seq analysis of survival cytokine genes expressed by all the cell types with >30 cells in LA or LP regions (left) and their receptors on Treg populations (right). b. NICHE-seq analysis UMAP visualisation of T-cell subsets (left) with overlay of Ccr5 and Ccr2 expression (right). c. Dot plot showing expression of Ccr2 and Ccr5 and their ligands (Ccl7 and Ccl8) in myeloid cells, T cells and ILCs isolated from the LA and LP NICHE-seq analysis. d. Localisation of Ccr2 (top left), Cxcr3 (top centre) and Cxcr4 (bottom left) expression in LA and LP by ST analysis on H&E (bottom centre). Violin plots of relative distribution of Ccr2, Cxcr3 and Cxcr4 expression (top right). Dot plot of Ccr2, Cxcr3 and Cxcr4 expression in the LA and LP by ST analysis (bottom right). e. Ligand-receptor analysis on Visium data. Adjusted p-values were calculated per spot using the package stLearn and displayed in the spatial context for particular ligand-receptor pairs (‘Ccl8_Ccr2’ and ‘Cxcl9_Cxcr3’) in two representative Hh samples (above, Hh mouse 2 and below Hh mouse 4). a-c: One sequencing run from 6 combined mice. d-e: Two representative samples of 4 individual mice per group (Hh and Hh/anti-IL-10R sequenced from two Visium slides.