Control eyes receiving only an ischemia-reperfusion insult were enucleated at 0, 1, 7, 14, or 28 days after reperfusion. Eyes with viral vector administration before ischemia-reperfusion treatment were enucleated at 7 days. All eyes were immediately fixed in 4% paraformaldehyde in phosphate-buffered saline (PBS) for 60 minutes. After they were rinsed with PBS, the eyes were frozen in optimum cutting temperature embedding compound (OCT; Miles Diagnostics, Elkhart, IN) and snap frozen in liquid nitrogen, after which they were stored at −80°C until sectioning. At cryosectioning, five serial sections (10 μm) were obtained at 100-μm intervals on each side of the optic nerve. Sections through the optic nerve were also taken, but optic nerve tissue was not included in cell counts. All specimens were processed for hematoxylin and eosin (Sigma-Aldrich, St. Louis, MO) staining.
The numbers of nuclear cells in the GCL, INL, and ONL were counted per 200-μm length at more than 10 points selected randomly. The mean cell count of these points was then used to determine a representative cell number for each layer.