Immunofluorescent Staining Assay of 3D Cell Culture of Colonoids Isolated from Mice Colon

Here, we describe immunofluorescent (IF) staining assay of 3D cell culture colonoids isolated from mice colon as described previously. Primary cultures developed from isolated colonic stem cells are called colonoids. Immunofluorescence can be used to analyze the distribution of proteins, glycans, and small molecules-both biological and non-biological ones. Four-day-old colonoid cell cultures grown on Lab-Tek 8-well plate are fixed by paraformaldehyde. Fixed colonoids are then subjected to antigen retrieval and blocking followed by incubation with primary antibody. A corresponding secondary antibody tagged with desired fluorescence is used to visualize primary antibody-marked protein. Counter staining to stain actin filaments and nucleus to assess cell structure and DNA in nucleus is performed by choosing the other two contrasting fluorescences. IF staining of colonoids can be utilized to visualize molecular markers of cell behavior. This technique can be used for translation research by isolating colonoids from colitis patients' colons, monitoring the biomarkers, and customizing their treatments. Key features • Analysis of molecular markers of cell behavior. • Protocol to visualize proteins in 3D cell culture. • This protocol requires colonoids isolated from mice colon grown on matrigel support. • Protocol requires at least eight days to complete.