UPDATE: the issue was the flow pressure being too high and cells being too sensitive to a loss of membrane integrity. I lowered the flow pressure and used a reagent/buffer that is designed to reinforce membrane strength.
Problem: I am culturing NIH 3T3 cells which are growing normally. They all look happy and healthy when I take them for flow cytometry after which I lose ~40% of my cell viability. I have never had this problem with my other cell lines e.g., MSC's. Could it be because of the change from the incubator 5%CO2 + 95%O2 to normal atmosphere air? Is there a specific temperature setting I should have my flow cytometer at other than room temperature? Should I change the flow pressure? If I don't perform flow cytometry my cells stay happy. My colleagues have run flow cytometry on their cell cultures (with other cell lines) and have not encountered any problems that I know of. Any thoughts?
Dear Genesis!
The survival of your cells after flow cytometry depends not only on the percentage of CO2 (rather on the time spent without CO2), because the medium is acidified, which affects the viability of the cells.
Secondly, the survival of your cells may depend on the reagents you use (antibodies, buffers, etc.). Check concentrations, conditions (temperature, humidity), shelf life.
The survival of your cells may also depend on the use of additional procedures, such as washing the cells with buffer or saline.
Most importantly, survival depends on the goals and objectives for which you are using flow cytometry on this culture.
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