Corneas were excised at 15 dpi and incubated in PBS-EDTA at 37°C for 10 minutes. Stromas were separated from overlying epithelium and digested in 84 U collagenase type 1 (Sigma-Aldrich, St. Louis, MO) per cornea for 2 hours at 37°C and then were triturated to form a single-cell suspension. Suspensions were filtered through a 40-μm cell strainer cap (BD Labware, Bedford, MA) and washed. Suspensions were incubated with anti-mouse CD16/CD32 (Fcγ III/II receptor; clone 2.4G2; BD PharMingen, San Diego, CA), then stained with various leukocyte surface markers for 30 minutes on ice. The following antibodies were used: PerCP-conjugated anti-CD45 (30-F11), PE-conjugated anti-CD4 (RM4–5), anti-IA/IE (2G9), APC-Cy7-conjugated anti-CD8α (53–6.7), FITC-conjugated anti-CD69 (H1.2F3), anti-CD25 (7D4), anti-CD11c (HL3), APC-conjugated anti-F4/80, biotin-conjugated anti-CD80, pacific blue-conjugated anti-CD8α, streptavidin-PE (all BD PharMingen); APC-conjugated anti-Gr-1 (RB6–8C5; Caltag, Carlsbad, CA), and pacific blue-conjugated anti-CD40 using a labeling kit (Zenon Pacific Blue; Invitrogen, Carlsbad, CA). All isotype antibodies were obtained from BD PharMingen. Intracellular staining for regulatory T cells was performed according to standard protocol using Foxp3 staining kit (eBiosciences, San Diego, CA). Briefly, after surface staining, cells were permeabilized using solution (Cytofix/Cytoperm; BD Biosciences, San Diego, CA) for 2 hours, then stained with APC-conjugated anti-Foxp3 (FJK16s; eBiosciences) for 30 minutes After staining, cells were fixed with 1% paraformaldehyde (PFA; Electron Microscopy Services, Fort Washington, PA) and analyzed on a flow cytometer (FACSAria with FACSDIVA data analysis software; BD Biosciences).