We are currently facing the problem that we can't do FACS analysis on isolated cells because they clot together after doing lavage with PBS and 3%FCS. How can we avoid that?
Yes, I'm well acquainted with the pains of trying to recover cells post-CLP, and then using the cells for functional assays! We do not use FCS for lavage; cold Hbss or PBS with 1mM EDTA or 10U/mL of heparin works fine. Strain the cells through a cell strainer to help remove cecal contents. Wash with Hbss/PBs with 0.5% BSA. There are ways to get rid of the bacteria and dead cells too.