Abstract
The myenteric plexus is located between the longitudinal and circular layers of muscularis externa in the gastrointestinal tract. It contains a large network of enteric neurons that form the enteric nervous system (ENS) and control intestinal functions, such as motility and nutrient sensing. This protocol describes the method for physical separation (peeling) of muscularis and submucosal layers of the mouse intestine. Subsequently, the intestinal layers are then processed for flow cytometry and/or immunofluorescence analysis. For complete details on the use and execution of this profile, please refer to Ahrends et al. (2021).