Sure, first doing microscopy and semiquantitative analyses of fluorescence and after that you can lyse cells and isolate RNAs.

We did it by preparing fresh tissue slices (as for in-vitro slice experiments) before analyzing RNA expression. You can check for fluorescence while keeping the slices alive in oxygenated ACSF in an electrophysiological recording setup equipped with a fluorescence microscope; if prepared well, fresh slices remain viable for many hours and RNAs do not degrade during this time.

Thanks Nora. Thats a good idea but my slides are already frozen (assuming its Ok to thaw them and then do microscopy?) and also we dont have electrophysiology equipments