I am very new to Flow, so please bear with me. I am trying to compare the DNA content between two samples, zygotes and macrogametes, to verify a purification method.

I think my gating process is okay: singlets (FSC-H vs. FSC-A or SSC-H vs. SSC-A) -> macrogametes or zygotes (SSC-A vs. FSC-A) -> DNA (Cy5-A vs. AF488-A/GFP-A, our organism is GFP strain and I used a Vybrant DyeCycle DNA stain). My controls are unstained zygotes and macrogametes (still express GFP, but not Cy5). But when I turn my DNA plots into histograms, it doesn't make sense to me. I know that my samples contain either macrogametes or zygotes as I check with microscopy before prepping for Flow, but I can't figure out how to show graphically that macrogametes are 1n and zygotes are 2n. Any advice is greatly appreciated!