I’m doing cell cycle in fixed cells. Does the method of fixation matter?

Answer

Fixation has two functions. First, it preserves the cells by preventing lysis and autolytic degradation. Second, it makes the cells permeable and thus their DNA accessible to impermeant DNA-binding dyes.
Precipitating fixatives (methanol, ethanol, acetone) are preferred for single color cell cycle staining. Disadvantages include some epitpoes are destroyed and there is more cell aggregation.
Crosslinking fixitves (-aldehydes) can have a harmful effect on stoichiometry of DNA staining, but fewer epitpoes are destroyed and less cell aggregation is induced. Although inferior in terms of stabilization & preservation of low molecular weight constituents within the cell, they adequately stabilize undamaged DNA.
You will need to choose the best fixation method for your application. Or you may use a cell-permeant dye such as the Vybrant DyeCycle stains or UV-excited Hoechst 33342 for cell cycle in living cells.