Once you determine the markers you want to investigate in your flow cytometry panel and the protocol you want to use, you will need to determine what fluorochromes are compatible with the staining, fixation and permeabilisation buffers you will use.

If you are interested in investigating markers within the cell, your cells may need to undergo treatments to make those antigens accessible to your staining reagents. Whether studying markers in the cytoplasm or nucleus, one will need to use various buffers for fixation and permeabilisation. It is important to consider how using different buffers affects the staining pattern of your markers and biological resolution of your data. 

Disclaimer: Results and conclusions shown throughout the Fluorochrome Faceoff are based on experiments performed under the conditions described. Users should evaluate reagents with their specific protocols as results may vary with different experimental conditions.