Proteomics analysis was performed on sclerae from genipin/HBSS (n = 3) rats at 4 weeks postinjection to determine the effect of genipin treatment on the abundance of various proteins involved in various functions, including protein binding, cell motility, and ECM structural support. Eyes were enucleated immediately after euthanasia and kept in cold PBS until processing. The sclera was first cleaned of conjunctiva, retina, muscle, and fat, and the RPE was gently peeled and scraped off from the sclera with a blade. The sclera was then washed in PBS, cut into smaller pieces, transferred to an Eppendorf tube, and frozen in liquid nitrogen. Frozen scleral pieces were ground using a CryoGrinder kit (OPS Diagnostics, Lebanon, NJ) and then suspended in 300 µl of lysis buffer (10 mM HEPES, 42 mM KCl, 0.1 mM EDTA, 0.1 mM EGTA, and 1 mM DTT; all from Sigma-Aldrich, St. Louis, MO), 1 × protease inhibitor from Thermo Fisher Scientific) and homogenized in a biomasher tube. Samples were sonicated on ice 3 times for 10 seconds and sodium dodecyl sulfate (SDS) was added for a final concentration of 2% (w/v). Samples were incubated at room temperature for 10 minutes to lyse the cells and extract the proteins, then spun for 45 minutes at 14,000 × g, at room temperature. SDS-soluble proteins were kept on ice, whereas SDS-insoluble proteins were processed further by adding 10 volumes of urea buffer (8M urea; 4% SDS, and 60 mM Tris-HCl; Sigma-Aldrich; 12.5 EDTA in deionized water) to samples, incubating 30 minutes at room temperature, and then centrifuging at 16,000 g for 5 minutes. Supernatant was precipitated using methanol/chloroform, resuspended on 2% SDS, and combined with SDS-soluble protein. Samples were reduced with dithiothreitol (DTT; 10 mM) at 60°C for 20 minutes, alkylated with iodoacetamide (IAA, 25 mM; Sigma-Aldrich) for 30 minutes at room temperature in the dark. The IAA was then quenched with DTT. Samples were precipitated using methanol/chloroform, and resuspended in digestion buffer (8M urea and 0.1M Tris pH 8.0) containing trypsin-Lys-C mix (Promega) and incubated overnight at 37°C. The following morning, 50 mM ammonium bicarbonate (Sigma-Aldrich) was added containing 1:40 trypsin/Lys-C and samples were incubated for 3 more hours with 10% trifluoroacetic acid (Sigma-Aldrich). Peptides were cleaned up using C18 tips (Nest Group, Southborough, MA), following manufacturer's instructions and dried by Speed Vac.