single cell RNA-seq on FACS purfied murine paneth cells
The small intestinal crypts harbour secretory Paneth cells (PCs) which express bactericidal peptides that are crucial for maintaining intestinal homeostasis. Considering the diverse environmental conditions throughout the course of the small intestine, multiple subtypes of PCs are expected to exist. We applied single cell RNA-sequencing of PCs combined with deep bulk RNA-sequencing on PC populations of different small intestinal locations and discovered several expression-based PC clusters. Some of these are discrete and resemble tuft cell-like PCs, goblet cell (GC)-like PCs, PCs expressing stem cell markers, and atypical PCs. Other clusters are less discrete but appear to be derived from different locations along the intestinal tract and have environment-dictated functions such as food digestion and antimicrobial peptide production Overall design: Paneth cells were purfied from the small intestine of mice using FACS, using positive markers c-KIT and CD24. Purified cells were used to perform single cell transcriptomics using 10X genomics, cellrangerd and seurat.