Fig. 1: Spatial transcriptomics reveals molecular regionalization of the murine colonic tissue in steady state.

a Schematics of the experiment: colonic tissue from a naive WT mouse (d0) was processed as a Swiss roll for spatial transcriptomic (ST) with Visium 10X technology (n = 1 Swiss roll). b Colon Swiss rolls shown in hematoxylin and eosin (H&E) staining (left) and with each ST spot color coded based on non-negative matrix factorization (NNMF) (right). ST spots belonging uniquely to one factor are colored in red, blue and green for NNMF1, 2 and 3 respectively. ST spots shared between different factors are colored with respective intermediate gradation of these 3 colors. c Top: spatial distribution of the 3 factors distinguishing muscle, lamina propria (LP) and intestinal epithelial cells (IEC). Bottom: heatmap showing the top 20 genes defining each factor. d Immunohistochemical staining of CDH17, TAGLN, ADH1 in healthy human colonic tissue (from Human Protein Atlas). e Digitally unrolled colonic tissue, showing the distribution of the 3 factors from Fig. 1c along the serosa-luminal and proximal–distal axis. f Proximal to distal distribution of Hmgcs2, Ang4 and B4galt1 expression in colonic swiss rolls (left) and digitally unrolled colon (right). g qPCR validation of regional expression of Hmgcs2, Ang4 and B4galt1 in proximal, mid and distal colonic biopsies from WT mice (n = 3, each dot represents one mouse). Data are presented as mean values ± SEM. Significance was assessed by one-way ANOVA with Bonferroni post-test. *p < 0.05; **p < 0.01. h Spatial distribution of 9 out of 20 factors in the naive colon displaying transcriptional regionalization along the serosa-luminal and proximal-distal axis. Each ST spot is assigned a color-coded score based on the expression of the genes defining each factor. i Schematic representation of the colon (top) and top genes annotated in Factors. Factors are grouped based on their proximal-distal distribution and color-coded (i.e. gray-pink-purple) based on their serosa-luminal distribution.