I am attempting to synchronize HEK 293 cells through serum deprivation (DMEM is the medium). When I analyze the results on a flow cytometer, however, the results do not show that a synchronization has taken place. I am using propidium iodide as dye and the FL2 channel of the blue argon laser (488 nm) with a 620 nm filter (the emission maximum of propidium iodide is around 617 nm) for analysis. Unfortunately, the serum-deprived samples have nearly as much of a second peak on the graph (representing the cells in mitosis) as the controls. Thinking that perhaps serum deprivation was not synchronizing the cells, I used Invitrogen's CyQUANT in order to determine cell proliferation after removing the serum. Sure enough, the HEK 293 cells had synchronized. Does anyone know what the problem could be with the flow cytometer analysis? I thought the alignment of the laser might have something to do with it, but why would only the serum-deprived samples have been affected (there was nothing wrong with the controls' graphs; only the supposedly synchronized cells showed an unnatural number of cells in mitosis, especially if they're supposed to be synchronized).
Edit: I forgot to mention, I'm analyzing them on FL2-Area.
Edited by Patience, 21 July 2009 - 05:47 AM.