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I support the response which warns against filtering, since it may very
well be true the clumps may represent an important subpopulation. Filtering
has its place, but only after all else fails.
We have done extensive work in the area of disaggregating solid tissues/tumors
through the years. The bottom line is - do what works. I would suggest -
if you haven't already - varying time and temperature, along with
trypsin concentration, to improve dissociation. There should be a
combination of conditions which will eliminate your clumps and still deliver
your cells intact and in good shape viability-wise (which should also be
a determining factor). Check out our manuscript - Ensley,J. et.al. Cytometry
8: 479-487, 1987 - which may speak directly to your problem since it deals
with disaggregation of head & neck squamous ca tissues for DNA/Ploidy
analysis.
MAK.
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