I never use the flow to count since we do not have a way to control the flow rate sample to sample without a calibrating beads as true count for example. However, if you want to check viability from different culture conditions, I suggest you to use trypan blue as a dye and look for changes on FL2 axis. Dead cells will be trypan blue positive. I have used a protocol that work very well. We prepare a 0,4% trypan blue solution in physiologic saline. Use 25 microliters of this solution plus 250 microliters of cell (bacteria, protozoan, etc) suspension.Incubate for 10 minutes at room temperature. Run into the cytometer using appropriate adjustments for SSCxFSC and the standard for FL1 and FL2 in your instrument.
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