I am working with a cell line that migrates very well in transwell migration assays, but when I try to do an invasion assay, the cells clump together within 2-3 hours after plating. I plate them at the same concentration at which I plate them for the migration assay, so I don't know why they clump during the invasion assay. I've tried using serum free as well as 0.05% FBS containing media and in both cases the cells clumped together. I have tried straining them with a 40 micron mesh to ensure the cells were well separated before plating and still they formed clumps which did not migrate. I usually plate 100,000 cells per insert which contains 50mcl of 1:5 diluted BD matrigel.
May be you can try will less cells or matrigel. This may help reduce the clumps.
Reducing the cell number may be a good idea. Do you have growth factors in the matrigel? You could try using growth factor reduced matrigel.
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