In a nutshell, is it possible to FACS a sample that is in oil rather than in a buffer (water based solution)? I would greatly appreciate any help with this. Thank you
It's possible that there's some specialized modified machine that can do it, but conventional flow cytometry machines can't do it. This article suggests one possible approach:
Unfortunately, FACS instruments are incompatible with nonaqueous suspensions, so to sort a water-in-oil emulsion, it is necessary to carry out a further emulsification to produce a water-in-oil-in-water double emulsion. The resulting sample, now dispersed in an aqueous phase, is amenable to FACS sorting.
There are also microfluidics machines that might be able to do it, but I think you'd have to build your own rather than being able to buy a solution (which would be expensive in any case, I think).