Extended Data Fig. 8: Validation of micro-niches by ST analysis and NICHE-seq.

a. Representative H&E image with manually annotated LA and LP from Hh/anti-IL-10R. b. Visual representation of cell cycle scoring of Hh (top) and Hh/anti-IL-10R (middle) treated gut swiss-rolls with quantification of S score (bottom left) and G2M score (bottom). c. Cell type decomposition of gut swiss rolls in Hh (left) and Hh/anti-IL-10R (right) treated mice. Dotplots showing NMF weights of cell types (columns) across NMF factors (rows), which correspond to tissue microenvironments (normalized across factors per cell type by dividing by maximum values). d. Identification of microglia/enteric neurone associated factor 5 (left) and LA associated factor 3 (right). e. Hh/anti-IL-10R swiss roll H&E. Localisation of LA associated factor 3 by NMF -based decomposition and its overlying RNA capture spots (top left). Localisation of LA and its overlying capture spot as defined by manual annotation (top centre and right). Localisation and normalized cell type abundance of eMBCs (bottom left), naïve CD8 + T cells (bottom centre) and LTi-like ILC3s (bottom right) in representative LA. f. Dotplot of Il10 and Il6 gene expression in the LA and LP by ST analysis (left). Violin plot of relative distribution of Il10 gene expression in the LA and LP by ST analysis (right). g. Cell type abundance in manually annotated LA and LP regions of Hh (top) and Hh/anti-IL-10R (bottom). Relative weights, normalized across LA/LP for every cell type. Cell type loadings represented by dot size and colour. h. Cell state enrichment (odds ratio) in the manually annotated LA vs the rest of the tissue in Hh (top) and Hh/anti-IL-10R (bottom). Statistically significant enrichments (chi-square test, p < 0.05) are shown in magenta-pink. Data show value ± SD. i. Cell state enrichment (odds ratio) in the manually annotated LA vs the rest of the tissue with muscularis mucosa removed in Hh (top) and Hh/anti-IL-10R (bottom). Statistically significant enrichments (chi-square test, p < 0.05) are shown in magenta-pink. Data show value ± SD. a-i: Representative of 4 individual mice per group (Hh and Hh/anti-IL-10R sequenced from two Visium slides.