Enucleated eyes were minced into small pieces and digested using a mixture of Liberase TL (0.1 mg/ml, #5401020001; Roche, Basel, Switzerland) and DNase I (0.2 mg/ml, #10104159001; Roche) in HBSS (14025-092; Fisher) at 37°C for 60 minutes with mechanical digestion at time 0, 30, and 60 minutes via a gentleMACS Octo Dissociator (130-095-937; Miltenyi Biotec) in C-tubes (130-096-334; Miltenyi). Cells were filtered through 40 μm nylon mesh in MACS Buffer (130-091-221; Miltenyi). Cells were spun at 350
g for 10 minutes and washed once in MACS Buffer. Erythrocytes were lysed using PharmLyse (1 minute, #555899; BD Biosciences) and washed once as above. Cells were stained for dead cells using Aqua Live/Dead (15 minutes,
Table) and washed twice. Cells were incubated with Fc-Block (20 minutes,
Table), stained with fluorochrome-conjugated Abs (30 minutes,
Table), washed twice, fixed with 2% PFA and washed twice. Data were acquired on an LSR II flow cytometer (BD Biosciences). Compensation matrices and data analysis were performed using FlowJo (Tree Star, Ashland, OR, USA). Approximately 3,000,000 singlet events were counted per mouse (2 eyes). First, singlet cells were identified and dead cells were excluded. CD45, a marker of leukocyte lineage, was used to identify leukocytes versus non-leukocytes. CD45
− non-leukocytes were gated on CD31 and CD140b to identify endothelial cells (EC) and pericytes, respectively. CD45
+ leukocytes were gated on CD11b
+ staining to identify mononuclear phagocytes and SiglecF, Ly6G, Nk1.1, B220, CD4, and CD8 negative staining to exclude eosinophils, neutrophils, NK cells, B cells, and T cells. Microglia have previously been shown to be CD45
dim and MHCII
low compared to infiltrating monocytes and macrophages.
16 Therefore, we used CD45
dim versus CD45
high to identify microglia from infiltrating cells. Microglia were identified in the CD45
dim group as CD64
+ and predominantly MHCII
low. In the CD45
high group, we identified CD64
−MHCII
− monocytes, CD64
−MHCII
+ dendritic cells (DC), and two populations of macrophages: CD64
+MHCII
− macrophages (MHCII
− Macs) and CD64
+MHCII
+ macrophages (MHCII
+ Macs). Fluorescence minus one controls were used to establish positive staining and gates (
Supplementary Fig. S1).