I am trying to collect peritoneal macrophages for experiments. I notice that when I take a lavage 6 days post thioglycollate injection, i.p and FACS phenotype them with F4/80 and Ly6G, I get primarily two populations - one F4/80 positive and one that is negative for both.

The F4/80 population is about ~37% and the negative one is the remaining ~63%. Publications are stating that it should be mostly macrophages at this point, so I need to troubleshoot on why my majority population is not F4/80+. Can anyone help?

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