Use a software that is Modfit LT Ver.2.0 (Verity software House, Topsham, ME).
The guideline will tell you how to do this in his handbook.
Be carefull as debris might be PI positive.
An easy way to get rid of debris (usually much smaller than cells) would be to plot FSC versus PI. Anything below a 2n DNA content with a small FSC would originate from debris containing DNA (or debris with relatively high autofluorescence). Anything above 4n would come from agregates (unless you work with any specific kind of tumor cells). This will give you a nice semi-diagonal distribution of you cells (small and 2n DNA = G0/G1, large with 4n DNA = G2/M, and everything inbetween will be S phase cells). If you want to look further in the cell cycle distribution you can had antibody against the phosphorylated form of histone H3, this will provide a way to discriminate G2 from M cells.
Hope this helps.
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