I am sorting a small population of cells (<5%) on a FACS Aria.
My issue is recovering the cells post-sort. On a good day I can get ~100,000 cells of my desired population, however, this small number of cells is extremely difficult to then quantitate (trypan blue exclusion). The cells do not pellet upon centrifugation.
It is really hard to get more cells (already sorting for HOURS to get 100,000) so aside from increasing sort time, does anyone have any suggestions?
Specifically, any thoughts on how to accurately isolate and count these cells?