Extended Data Fig. 5: FACS cell sorting of photoactivated cells and tissue memory heterogeneity.

a. Representative images of pre- and post-photoactivation of LA (top) and T cell zone of CP (bottom). b. Gating strategy of cell sorting by FACS of GFP+ cells in the caecal patch (top left), MLN (bottom left) and caecum LA and LP (right). GFP gate set on un-photoactivated samples. c. UMAP visualisation of total cell subsets (left) with detailed cell type annotations (right). d. Bar chart showing total cell subsets across all tissue niches (top left) and cell numbers (bottom left). UMAP visualisation of cell lineages by gut region (bottom right). e. UMAP of CD4 memory, Th17, and gd T cells subsets (top). Overlap of cell location (bottom). f. Gene overlays of CD4 memory subsets from all tissues. g. Gene expression of canonical Th1 and Th17 genes expressed by the CD4 memory subsets. h. Frequency bar chart showing the subsets of CD4 T cells in the LA and LP. a-h: Representative of 6 combined mice.