I usually look at microglia isolated from mice brain using the standard percol gradient method without using Collagenase/DNAse steps i.e. just meshing the brain with 10 ml syringe plunger and then layering 30% brain cell suspension on 70% percol. This is the way I look for infiltrating lymphocytes (CD45 Hi) and microglia (CD45 Int CD11b+ cells) by Flow cytometry. The method works well for analyzing infiltrating lymphocytes but for microglia, I get the fluctuating data for the mice even within the same group. Is there any other clean and better way to isolate and characterize microglia from mice brain? Waiting for your suggestions.