RNA-seq on FACS sorted paneth cells from the murine duodenum, jejunum and ileum

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 cells RNA-sequencing of PCs combined with deep bulk RNA-sequencing on PC populations of different locations (duodenum, jejunum, ileum) and discovered several expression-based clusters. Some of these are discrete and resemble tuft cell-like PCs, goblet cell-like PCs, PCs expressing stem cell markers, and senescent PCs. Other clusters are less discrete, but based on bulk RNA-seq appear to be derived from different locations along the small intestinal tract. Furthermore, a comprehensive spatial analysis was conducted using the Resolve bioscience technique, identifying different PCs clusters along the small intestine, but not along the crypts themselves. We isolated PCs from the three regions using a pool of 8 mice, and repeated this in total 4 times independently. RNA as isolated and sequenced followed by differentail gene expression profiling