Dear Abhinav,
IHC and Fluorescent are two different techniques which demand different protocol to do. Basically, in both of them, Paraffin sections work very well.If you are doing Immunofluorescence staining then you should use fluorescent conjugated secondary antibody and if you are doing IHC you should use biotinylated secondary antibody. also choosing proper detergent based on expression area (intracellular or surface marker) you should choose the triton or tween.
hope these help you, let me know if I can be further help.
it shouldn't make a difference, as your flourecent stain will be added to the slice with exposed targets.
all the best
IHC (Flouresence or not) will work with both parafiin embedded and cryostat sectioned blocks. You just have to add an additional step of depraffinization with paraffin embedded tissue. But it saves a lot of space over cryostat cut tissue that needs to be kept in the frozen. So weigh your options before you start. As for staining, it should work on both.
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