I'm about to start troubleshooting our CLARITY process and came across this paper for achieving very nice antibody staining in whole mount tissues. Granted, their mouse corneas are only 120µm thick (which is nothing compared to whole organs), but the principle they used sounds promising...
Here's the paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2650717/?report=classic
I'm curious, for those who have experience, if you think the cleared tissue samples would tolerate this protocol? Or if an additional embedding/electrophoresis step would just obliterate the sample? Passive diffusion just seems like a losing battle between enough permeabilization for staining versus sample destruction.