I'm not sure about that. It depends on how well your cells handled the freeze initially as well as how they handle being thawed. My concern is that the cells may lyse when you increase the temperature from -80 to ambient temperature. Check them and see how they look after you isolate them. I have successfully isolated proteins and enzymes from cells frozen at -80.
I would not recommend to analyze these cells by FACS. After freezing, the quality of obtained results will be compromised in any case.
The key will be to separate out the dead cells from the analysis and focus only on the live. Since freezing would damage the membrane, your cells would probably stain falsely positive if you would use a membrane impermeable viability dye. So, if you have a dead cell marker that is not based on the membrane being intact for exclusion, you may be able to do it. The problem with dead cells is that they have higher autofluorescence so they can cause problems in subsequent analysis steps of other markers.
Yes of course we have analysed -80 frozen in 10% cryoprotectant many times, I think the trick to reduce debris and dead cells during FACS is to use a 70um filter to prepare cells and set 20000- 25000 threshold in FACS diva while acquisition
Following on from Aditya's reply what I've seen in creating dead cell controls using 70% EtOH is that the cells become sticky and you get a doublet smear with high FSC (the filtering would reduce the appearance of doublets) and with using 1% Triton X100 is that the cells fragment and reduce their FSC (which is why a higher FSC threshold would help).
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