Paneth cell scRNA-seq analysis of un-infected and Salmonella Typhimurium infected mice

Paneth cells consist of heterogeous phenotypes. How Paneth cells respond to infection by invasive pathogenic bacteria at single cell level remains uncharacterized. We used a flow cytometry based method to isolate Paneth cells from uninfected and Salmonella-infected Paneth cell reporter mice (Lyz1-3'UTR-IRES-CreER; Rosa26R-tdTomato). These highly pure Paneth cell populations were used for single cell RNA sequencing analysis. Paneth cell reporter mice (Lyz1-3'UTR-IRES-CreER; R26R-tdTomato) were intraperitoneally injected with a single dose of tamoxifen to activate the tdTomato reporter. One day after, mice were orally administered with 15mg of streptomycin. One day after, mice were divided into two groups (uninfected and infected), which were orally inoculated with sterile PBS (as control) or 10^8 CFU Salmonella. Four days after infection, tdTomato+ Paneth cells were isoated from ilea of uninfected and infected mice, and processed for single cell RNA sequencing by 10xGenomics. S. Typhimurium orally administered with 15mg of streptomycin, followed by oral infection of PBS (ABX) or 108 CFU S. Typhimurium (SAL) 24 h later., Salmonella-infected mouse (4 days infection) and analyzed by scRNA-seq