I have been having some problems with my western blots dealing with apoptosis. I'm focusing on isolating bands for caspase 9 in untreated cells and cells infected with Trichomonas vaginilis for 6 hours, however every time i run my western, the control bands are much darker than the infected. Before lysing, I run my infected cells through an apoptotic separator to isolate them. I have been running the gels with 20 micrograms of protein in each lane. Does anyone have any ideas why the infected cells have lighter bands than control? Thanks in advance.