Fig. 4: Single-cell atlas of gene expression and chromatin accessibility in the human intestine.
From: Organization of the human intestine at single-cell resolution
a, Sections of the intestine analysed by separate snRNA-seq and snATAC-seq experiments or multiome experiments. b,c, UMAP representation of all snRNA stromal (b) and immune (c) cells coloured by cell type. DC, dendritic cells; fib., fibroblasts; ILC, innate lymphoid cells; myofib., myofibroblasts; SM, smooth muscle cells. d, UMAP representation of snRNA epithelial cells in the four primary regions of the intestine. Jejunum includes both proximal- and mid-jejunum samples. Colon includes samples from the ascending, transverse, descending and sigmoid colon. e, Expression of INSL5 and the INSL5 receptor, RXFP4, in different cell types in different regions of the intestine. RXFP4 was expressed in less than 2.5% of all epithelial cell types that were not included in the dot plot. C, colon; D, duodenum; I, ileum; J, jejunum; enterochrom., enterochromaffin cells; enteroendo., enteroendocrine cells. f, Beeswarm plot showing the log-transformed fold change between the small intestine and colon for groups of nearest-neighbour cells from different cell type clusters. Significant changes are indicated in red and blue. Lymph. endo., lymphatic endothelial cells. g, Subclustering of specialized secretory cells in d coloured by cell type. h, The expression of secretory genes in specialized secretory cells defined in g. i, The percentage of MUC6+ enterocytes among all cell types for the four donors imaged using MUC6 antibodies. j, Representative CODEX fluorescence image of the duodenum (6 out of 57 markers overlaid) (left). Hoechst (nuclei), MUC6, MUC1 (also found in gland areas), cytokeratin (pan-epithelial), α-SMA (muscle) and vimentin (stromal) staining is shown. Right, the magnified area highlights the gland just below the mucosa in the submucosa. This experiment was independently repeated four times. Scale bars, 500 µm (left) and 50 µm (right).
