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View submission: Trypan viability test, What about dead cells ?
The process of trypsinizing alone would get rid of many of the dead floating cells, unless the OP continued to collect the supernatant and PBS washes like they described in their post. The other potential issue with this approach might be if the final volume in OP's tube made the cells too dilute to accurately count. Ideally, there should be ~25-100 cells per hemocytometer quadrant in order to get the most accurate counts.
OP, you've come up with a good solution to this issue even though it's tedious. I do a lot of cell proliferation assays with adherent cells + trypan blue, and think about the issue of viability underestimation quite a bit. Not sure if this would be possible for your experiment, but one thing that might help is to assess viability over a period of multiple days. If the number of viable cells in a given condition declines over time, relative to the number of cells you started with, then this is a pretty good indication that the cells are dying. Of course, it's always a good idea to have a couple of assays that come to the same conclusion though.
There's nothing here!