Aqueous and vitreous were collected and pooled from 15 eyes from each treatment group. Samples were collected from naïve animals on day 0, from PMU on day 2, and from EAU on day 14. These time points were chosen for the animals with uveitis, as these times correlated with maximal inflammation observed in each model (data submitted in accompanying manuscript). From individual eyes, aqueous was aspirated and protease inhibitor added. The vitreous was separated from the retina, diluted in 150 μL PBS and 1X protease inhibitor (Sigma-Aldrich Corp., St. Louis, MO, USA), and homogenized. The sample was spun down for 1 minute at 16,000g, and supernatant was collected. All samples were stored at −80°C before testing. From half the pool, protein was precipitated by adding an equal volume of 20% trichloroacetic acid and incubating on ice for 30 minutes. The samples were centrifuged at 4°C for 15 minutes at 16,000g, and the supernatant was discarded. The pellet was washed two times with acetone and then centrifuged at 4°C for 5 minutes at 16,000g. Protein resolubilization was achieved with ReadyPrep Rehydration Sample Buffer (8 M urea, 2% CHAPS, 50 mM dithiothreitol, 0.2% Bio-Lyte 3/10 ampholytes, trace bromophenol blue) from Bio-Rad (Hercules, CA, USA) for traditional 2-D gel electrophoresis and in buffer containing 7 M urea, 2 M thiourea, 30 mM Tris, 4% CHAPS, pH 8.5, for differential gel electrophoresis (DIGE). Protein concentration was measured by Pierce 660 nm Protein Assay from Thermoscientific (Rockford, IL, USA).