3' droplet-based single cell RNA sequencing of a mouse large intestinal epitherlium

Using 3' droplet-based single-cell sequencing, we performed the transcriptional profiling of mouse large intestinal epithelial cells at the single-cell level. For scRNA-seq of the mouse colonic epithelium, we isolated mouse colonic crypts from three female 12-week-old C57BL/6 mice. For purification of epithelial cells and removal of immune cells and dead cells, the cells were suspended in 200 ml of cold PBS and stained with 5 ml of APC anti-mouse CD326 (EpCAM) antibody (118213, BioLegend), PE anti-CD45 antibody (BD Biosciences, 1:500) and DAPI (1:1000) for 20 min. Live CD45– EpCAM+ single cells were sorted into a 1.5 mm tube using a cell sorter.