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Cells from the colon and small intestine lamina propria were isolated as previously described^{8 (link)}. The cells were stimulated and stained as previously described^{8 (link)}. The following antibodies were used for surface staining of: CD3 (145-2C11, eBioscience); CD4 (L3T4, BD Difco); CD11b (M1/70, eBioscience); CD11c (N418, eBioscience); F4/80 (BM8, eBioscience); CD103 (M290, BD Difco); major histocompatibility complex (MHC) II (M5/114.15.2, BD Dico); TCR-γδ (eBioGL3, eBioscience); and NKp46 (29A1.4, eBioscience). Intracellular cytokine staining was performed using IL-17A (TC11-18H10, BD Difco) and IL-22 (IL-22JOP, eBioscience) antibodies. All antibodies were used at final concentration of 1 μg/ml. The cells were analyzed using a Gallios flow cytometer (Beckman Coulter, Brea, CA, USA). Leukocytes were gated using forward scatter (FSC) and side scatter (SSC), and within the leukocyte gates, the innate immune cells were identified as macrophages (MHCII⁺F4/80⁺CD103⁻CD11b⁺CD11c⁻) or dendritic cells (MHCII⁺F4/80⁻ CD103^+/−CD11b⁻CD11c⁺). For the lymphoid compartment, the leukocytes were gated using FSC and SSC. Within the lymphocyte gate, the populations were identified as T_H17 cells (CD3⁺CD4⁺IL-17⁺IL-22⁺), T_H22 cells (CD3⁺CD4⁺ IL-17⁻IL-22⁺), NKp46⁺ ILCs (including ILC3 and NK cells; CD3⁻CD4⁻NKp46⁺), LTi cells (CD3⁻CD4⁺NKp46⁻), γδ T cells (CD3⁺CD4⁻TCRγδ⁺) or CD3⁻CD4⁻NKp46⁻ cells.

Retinas were digested using the Papain Dissociation System (Worthington), incubated for 2h at 37°C in collaganase (80U/ml; Sigma-Aldrich), and cells collected. Six retinas of three IL17A-GFP mice were pooled for flow cytometry analysis of IL-17A. Cells were incubated with anti-mouse CD16/32 antibody (Fc block; eBioscience), and anti-mouse CD4 (T cells; GK1.5, eBioscience), anti-mouse Ly6G (neutrophils; NIMP-R14, Abcam), anti-mouse NK1.1 (NK cells; PK136, eBioscience), anti-mouse TCR ( T cells; eBioGL3, eBioscience), or anti-mouse F4/80 (macrophages; 521204, R&D). Alternatively, cells were incubated with anti-mouse/human antibodies: Vimentin (Muller glia; EPR3776, Abcam), ROM-1 (Photoreceptor cone cells; Aviva), and IL-17RC (R&D). Cells were analyzed using a C6 Accuri flow cytometer (BD); gates were set to isotype controls, and compensated using FlowJo.