So let's say I have 3 samples and I am interested in testing different fluorophore-conjugated antibodies against certain antigens by using 12 different colors. Howeveer, aach sample only has 10 colors (out of the 12 possible colors) against certain antigens and each color panel is different (i.e. color X against antigen A in the first sample is different from color Y against antigen A in the second sample).
1) Can I run all my samples in the same experiment assuming I have all 12 single stain controls for compensation and appropriately label my color combinations while running samples?
2) If so, let's mention that color X and color Y are excited by the same laser and detected by the same BP filter... will this interfere with my data?
So.... yes... provided...
1) Your cell population has to be the same, because how you gate on your FSC and SSC will affect compensation.
2) Also, it's not the filter that you have to worry about exactly, it's the emission wavelength overlaps. It's doable, but the compensation will take a bit of work.
3) And I would suggest you also run the Fluorescene minus one controls... for this many colors.
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