Mouse duodenal and ileal Paneth cell single cell RNA sequencing

An indepth analysis of Paneth cell transcriptome at single cell level has not been available. Existing intestinal epithelial cell scRNA dataset contain many cell types, where Paneth cells represent a small portion. We used a flow cytometry based approach to enrich and isolate relatively pure Panethc cells from a newly developed Paneth cell reporter mouse line (Lyz1-3'UTR-IRES-CreER; Rosa26R-tdTomato). Single cell RNA sequencing was performed on purified duodenal and ileal Paneth cells of mice housed under specific pathogen free condition. Paneth cell reporter mice were intraperitoneally injected with a single dose of tamoxifen dissovled in corn oil. 48 hrs later, mice were sacrificed, duodenal and ileal crypts were isolated, digested into single cell suspension, and subjected to flow cytometry sorting of viable tdT+ cells. Viablity and purity of duodenal or ileal Paneth cells were confirmed by flow analysis. A total of 6626 duodenal and 6893 ileal Paneth cells were processed for library construction and single cell RNA sequencing by 10xGenomics.