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3 protocols using ghost dye

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Isolation and Analysis of Immune Cells

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Tongues were harvested and digested with Collagenase IV (0.7 mg/ml) in Hanks’ balanced salt solution for 30–45 mins at 37°C. Cells were separated by Percoll gradient centrifugation. Abs were from the following sources: anti-CD45 and anti-CD11b (BioLegend), anti-CD4 and anti-F4/80 (Invitrogen), anti-TCRβ, anti-CD8, and anti-CD19 (eBioscience), and anti-Ly6G and anti-Ly6C (BD Biosciences). Dead cells were excluded using Ghost Dye (eBioscience). Data were acquired with an LSRFortessa and analyzed using FlowJo software (TreeStar).
Collected single-cell suspensions from LN were filtered and dead cells were excluded using Ghost Dye (eBioscience). LN were cultured in complete medium (RPMI media containing 10% FCS, supplemented with L-glutamine and antibiotics) with 50 ng/ml PMA and 500 ng/ml ionomycin (Sigma-Aldrich) in the presence of Golgiplug (BD Biosciences) for 4 h, followed by staining with Ghost Dye, CD4 and IL-17 (Biolegend).
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2

Multiparameter Analysis of Kidney Cells

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Frozen sections (8 μm) were fixed in 100% methanol and blocked with 5% goat serum (500622, Life Technologies) in Triton X. Primary antibodies were incubated overnight: C/EBPδ (Abcam, 1:200), normal rabbit IgG (Abcam, 1:200), C/EBPβ (Abcam, 1:200) and rabbit monoclonal IgG (Abcam, 1:200). Slides were incubated with goat anti-Rabbit Cy3 antibody (A15020, Thermo Fisher) or DAPI. Slides were visualized on an EVOS FL microscope (Life Technologies).
For flow cytometry, kidneys were harvested following perfusion with PBS. Cells were digested with collagenase IV (1mg/mL) in HBSS. Antibodies: anti-CD45 (clone 30-F11, Thermo Fisher), anti-Ly6G (clone 1A8, BD Biosciences), anti-Ly6C (clone HK1.4, eBioscience), anti-CD11b (clone M1/70, BioLegend), anti-CD133 (clone 13A4, Thermo Fisher), anti-C/EBPδ (Abcam, 1:500), rabbit polyclonal Abs (Abcam, 1:500), and secondary goat anti-Rabbit Alexa Fluor 488 Abs (Thermo Fisher). Dead cells were excluded using Ghost Dye (eBioscience). C/EBPδ intracellular staining was performed with the FOXP3 staining kit (eBioscience). Data acquired with LSR Fortessa and analyzed using FlowJo software (TreeStar).
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3

Comprehensive Immune Cell Profiling

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CNS tissue homogenates were incubated in digestion medium containing 0.5 mg/mL collagenase type I (Worthington Biochemical) and 1000 U/mL DNase I (Sigma-Aldrich) for 45 minutes following myelin debris removal using a Percoll gradient. LNs were incubated in digestion medium RPMI supplemented with 0.1 mg/mL DNase I (Invitrogen) and 0.1 mg/mL Liberase (Roche). Collected single-cell suspensions were filtered. Resulting cell suspensions were incubated with the following antibodies: anti-CD45 (clone 30-F11, Thermo Fisher Scientific), anti-Ly6G (clone 1A8, BioLegend), and anti-Ly6C (clone HK1.4, BioLegend). Dead cells were excluded using Ghost Dye (eBioscience). For cytokine analysis, LNs were cultured in complete medium (RPMI media containing 10% FCS, supplemented with l-glutamine and antibiotics) with 50 ng/mL PMA and 500 ng/mL ionomycin (Sigma-Aldrich) in the presence of GolgiPlug (BD Biosciences) for 4 hours followed by FACS staining. Cells were stained with Ghost Dye, CD4 (clone GK1.5, BioLegend), IL-17 (clone TC11-18H10.1, BioLegend), IL-10 (JES5-16E3, BioLegend), and IFN-γ (XMG1.2, BioLegend). To assess T cell differentiation, in vitro differentiated CD4+ T cells were stained with Ghost Dye, CD4 (clone GK1.5, BioLegend), and IL-17 (clone TC11-18H10.1, BioLegend). Samples were acquired with BD LSRFortessa and analyzed using FlowJo software (Tree Star).
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