PI can be used to gate out dead cells in combination with PE and FITC staining (see Sasaki et al, Cytometry 8:413-420, 1987). It is probably advisable to use a low concentration of PI. Sasaki used 0.5 ug/ml, but I have seen protocols using up to 5 ug/ml, but not the higher concentration of 50 ug/ml used for cell cycle staining. Since you are gating out the PI positive cells and analyzing the negative cells, the spectral overlap between PI and PE is not significant. Hope this helps, Tony Bakke, Ph.D. Director, Clinical Immunology and Flow Cytometry Lab Oregon Health Sciences University
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