Hi - I just re-read what you wrote and realised I maybe did not answer your question...(I was thinking about single cells rather than tissue sections). As the tissue is already PFA fixed then it may be that (depending upon storage) you might not get any decent RNA out of a single cell - unless during embedding/fixing care was taken to try to preserve RNA then it may already be too degraded for RNA analysis.
(this paper discusses best fixatives for tissues for later RNA extraction: http://onlinelibrary.wiley.com/doi/10.1 ... 0/abstract
I am guessing that the section is blocked in wax? If so then you will probably have to remove this from the section prior to isolating the cells. Normally the section would have been dehydrated etc prior to embedding in wax so really the reverse if this is required (re-hydration). As during wax embedding the tissue would have been subject to graded ethanol baths (70 - 100% ETOH) then I am suprised there is still GFP signal there to be honest.
To re-hydrate a section I would normally place a section on a slide into heated Histoclear (a non-toxic xylene substitute) to remove the wax then re-hydrate (90% ETOH, 70% ETOH, 50% ETOH, H2O) at 2-5 min per bath.
The heating steps above may prove problimatical if using a membrane slide (as the membrane may melt).
As regards section sizes - as the wax will be removed during the clearing (above) then this should not affect cutting BUT bear in mind that cells (rounded) range in size from around 10 microns to 20-25 microns. This means that sections less than 30 microns will probably not contain very many intact cells but instead will be cell "slices".
At best and remaining RNA in your fixed tissues will probably be <700 bp (DNA which is "tougher" is usually reduced to 500-700bp fragments by fixation/dehydration/embedding).
In brief: The approach you are taking is unlikely to work unless the samples were fixed and blocked in wax following a protocol designed to preserve RNA integrity (see paper ref above which fixes in methacam which would probably destroy any GFP signal anyway).
What you could do is try to see if you can get a protocol that gives at least some info: (assuming the sections are in wax and you have an LCM with seperate cell cutting and "pinging").
i.e: Cut 50 micron sections. Place on membrane slide. Isolate 100 cells, 10 cells and 10x 1 cell directly into seperate collection devices (tube or lid). Place RNA lysis buffer (with no enzyme in) into tubes and heat to 70oC (to melt residual wax in the sections) and isolate RNA using desired columns etc. Perform rt (reverse transcription/pre-amp) PCR using control primers only (not sample) with the primers for the gene (such as 28S) being no more than 200 -300 bp apart.
This will tell you a rough limit of detection and if this has any chance of working.
If any of the assumptions I have made are wrong then let me know.