There is a major difference between fixing and storing samples for DNA analysis and for surface marker analysis. DNA content will remain largely the same, sufficient at least for PI cell cycle analysis. However, surface markers that are native/"live" and fixed can have different antigenicities even without storage because the flexibility of the marker will lessen from the fixation alone. Ultimately, the answer to this will have to be determined empirically and will depend on:

Because your sample is fixed, I wouldn't actually worry too much about degradation or anything like that, so long as the temperature is cool on storage. You should do a trial run to see if your fresh sample and a fixed/overnight-stored sample give you the same result (split the same sample into two). If it looks the same, then you could probably store samples for maybe 1-2 weeks at 4 degrees prior to analysis (if your prep is very clean and well-fixed). The sooner you analyze, the better, of course.

Thanks Jordan for your input. I have already started the experiment you suggested. I would like to just add one more point here that you might have missed in my question. I have said that for the same antibody I am regularly fixing the ES/iPS cells, storing them at 4 degree (for one week) or -80 degree (for several weeks) and then processing them for I-FISH and results are perfect. That is why I was thing to do the same for FACS and trying to seek opinion if anyone has done it.

Thanks again.

Hi Shafqat, 

Please can I ask if you tried doing FACS on ES cells which were PFA fixed and then frozen for storage?  I am looking to do intracellular staining and FACS on this type of sample and wondered if it worked?

Thank you

Hi Rosanna,

I did it once but cell no was very low and it failed. I will do it again with in a month mostly and lets see what comes out. Sorry for being unable to give you any input.