I'm doing a differentiation experiment with flow analysis, comparing two cell lines: one is the wt cell line, and the other is a stable line transduced with our GOI + GFP marker.

The GFP is just a marker and is not important for my experiment.  Can I leave the GFP uncompensated?  The panels I'm using are:

(1st panel) PerCP-Cy5.5(Blue A), PE-Cy5(Y/G C), Alexa700(Red B), and sytox orange(Y/G E).

(2nd panel) APC(Red C), APC-Cy7(Red A), and sytox orange(Y/G E).

I checked the spectra and it doesn't look like GFP will overlap with the other fluors?  Also, I'm worried that I can't really compare the GFP- cell line with the GFP+ cell line if I compensate for GFP; it might overcompensate the GFP- cells.   

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