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.