Gene expression profile at single cell level of immune cells and structural cells from the epithelial layer, and immune cells from the lamina propria layer of the small intestine

The single-cell suspensions of two major intestinal compartments, the epithelium layer and lamina propria layer, were purified from C57BL/6J mice fed a chow diet and a HFHS diet for 10x Genomics Chromium scRNA-seq analysis. Small intestines were isolated from ten C57BL/6J mice fed a chow diet and ten mice fed a HFHS diet for 8 weeks. The single-cell suspensions of two major intestinal compartments, the epithelium layer and lamina propria layer, were purified and then subjected to FACS sorting. For intraepithelial and lamina propria immune cells, cells were sorted for CD45.2+ live cell population and then profiled utilizing droplet-based 10x Genomics Chromium scRNA-seq. For additional lamina propria immune cells, CD45.2+ live cells were sorted from the lamina propria layer of a new cohort of ten chow diet mice and ten HFHS diet mice, and then profiled using droplet-based 10x Genomics Chromium scRNA-seq. For structural cells, non-hematopoietic CD45.2- live cells were sorted from the epithelium layer of a new cohort of ten chow diet mice and ten HFHS diet mice, and then profiled using droplet-based 10x Genomics Chromium scRNA-seq.