Immunofluorescence localization was performed as previously described.
31 Briefly, corneas were fixed with cold methanol or 4% paraformaldehyde in PBS, cryoprotected with sucrose-PBS in a series of dilutions (10%, 20%, and then 30%), embedded and frozen in OCT medium (Sakura Finetek, Torrance, CA, USA). Cross sections of 6 μm were cut using a cryostat (Microm HM 505E; GMI, Ramsey, MN, USA) followed by immunofluorescence localization. For corneal flat mounts, freshly enucleated corneas were removed under an operating microscope (Carl Zeiss Microscopy, Oberkochen, Germany). Cornea flat mounts were digested in 1 mg/mL collagenase solution (Worthington Biochemical Corporation, Lakewood, NJ, USA) in PBS for 7 minutes at 37°C to facilitate antibody penetration into the tissue. No collagenase was used for BrdU or Ki-67 flat mounts which were fixed in cold methanol. For BrdU staining, tissue was treated with 2N HCl at 37°C for 15 minutes to denature DNA and neutralized in boric acid (pH 8.5) 3 times for 5 minutes. Sections and flat mounts were then blocked with 5% bovine serum albumin (BSA) and then incubated overnight at 4°C in anti-nestin at 1:100 (Sigma-Aldrich Corp.), anti-nerve growth factor receptor p75 at 1:100 (Chemicon, Temecula, CA, USA), anti-Sox9 at 1:100 (Chemicon), anti LGR5 at 1:150 (Abcam, Cambridge, MA, USA), anti-Ki-67 at 1:100 (Dako, Denmark) and anti-BrdU (ab-6326, Abcam) followed by Alexa Fluor 565-conjugated goat anti-rabbit IgG or goat anti-rat IgG (Molecular Probes, Eugene, OR, USA) at 1:200. Alexa Fluor 594 phalloidin (Molecular Probes) also was used. Flat mount corneas were divided into 4 symmetrical quadrants. Positive and negative controls were processed in parallel. The nuclei were counterstained using Vectashield mounting solution with DAPI (Vector Lab, Inc., Burlingame, CA, USA). Corneal flat mounts double staining was performed by incubating tissue with primary antibodies overnight. Secondary antibodies were added together and incubated for one hour. Images were captured using a confocal laser-scanning microscope (FV1000 MPE; Olympus America, Inc., Center Valley, PA, USA) with a ×40 or a ×60 1.42 NA oil immersion lens. To avoid bleed-through between fluorescence emissions, samples were scanned sequentially with 488- and 543-nm lasers, and emissions were collected with appropriate spectral slit settings.