High-yield enrichment of mouse small intestine intraepithelial lymphocytes by immunomagnetic depletion of EpCAM(+) cells

Lymphocytes in the mouse small intestine (SI) epithelium are critical to establish effective barrier immunity. Here, we describe a magnetic cell separation protocol that employs anti-epithelial cellular adhesion molecule (EpCAM) antibodies to deplete epithelial cells and to enrich for intraepithelial lymphocytes (IELs) from SI tissues. The resulting IEL preparation was functionally and phenotypically comparable to IELs isolated using conventional density gradient centrifugation protocols. Moreover, the yield and purity of anti-EpCAM-depleted SI IELs were higher than those enriched by conventional isolation. For complete details on the use and execution of this protocol, please refer to Prakhar et al. (2021).