Fig. 1: A cellular and spatial atlas of the mouse colon across regions and ages.

Study design overview. a, Sampling time points: birth/juvenile (0–4 weeks), adulthood (6–12 weeks) and aging (6 months–2 years). b, Sampling regions: proximal, middle and distal colon. c, Spatial atlas. The t-distributed stochastic neighbor embedding (t-SNE) embedding of 66,481 ST spot profiles colored by age group (left), colon section (center) and MROI (right), along with relative abundances (stacked bars; bottom). d, Single-nucleus atlas. The t-SNE of 352,195 snRNA-seq profiles colored by cell type cluster (top) and their relative abundances (stacked bars; bottom). e, Analysis. Multitissue dataset (bottom left) served as input to cSplotch, which uses histological (MROI and semantic segmentation) and expression (ST and snRNA-seq priors) data to estimate the abundance of each snRNA-seq cell type in each spatial spot and then uses hierarchical Bayesian modeling (cSplotch model) to infer cell-type-specific gene expression conditioned on age, region, sex and MROI annotation (results).