Abstract
Herein, we provide a protocol describing the preparation and labeling of cells in mouse esophageal epithelial whole mounts. We include details of tamoxifen administration used to genetically label and trace the fate of basal cells. We demonstrate how EdU incorporation alone or in combination with additional markers can be used to assess in vivo cell cycle progression or stratification dynamics. Finally, we highlight how optimization of cell labeling is required for reproducible analysis. For complete details on the use and execution of this protocol, please refer to Grommisch et al.1.