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1

Fluorophore-conjugated antibodies for flow cytometry

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Fluorophore-conjugated murine antibodies were purchased from eBioscience, including antibodies specific for CD8a (53–6.7; catalog #48-0081-80), Thy1.1 (HIS 51; 25–0900-82), Tim3 (RMT3-23; 14–5870-81), Lag3 (ebioC9B7W; 12–2231-81), CD137 (17B5; 17-1370-80), KLRG1 (2F1; 175893–81), and CD25 (PC 61.5; 17–0251-81). Other antibodies to FasL (K10; 106805), vβ9 (MR10-2; 553201), CD69 (H1.2F3; 104502), CD127 (A7R34; 135013), CD80 (16-10A1; 553768), CD86 (GL-1; 105011), IL-2 (JES6-5H4; 503807), IFNγ (XMG1.2; 505809), TNFα (Mab11; 502913), Bax (6A7; 633801), and Bcl-2 (10C4; 633507) were purchased from Biolegend. 7AAD (A1310) and other antibodies were purchased from BD Biosciences, including Fas (Jo2; 563647), Thy1.2 (53–2.1; 561616), CD103 (M290; 557495), purified rat anti-mouse CD16/CD32 (2.4G2; 12–4875-80), PD-1 (J43; 11–9985-81), and Vβ8.1/8.2 (553185). Antibodies against pAKT (S473; D9E; 5315S) were purchased from Cell Signaling Technology. Anti-Eomes (DAN11 mag; 12–4875-80) and the LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (L34957) were purchased from ThermoFisher. For FasL detection, Panc1 cells were treated for 24 h with 3 µg/ml Batimastat (BB-94; ab146619) purchased from Abcam. Flow cytometry data were acquired on a BD FACS Canto II instrument or LSR II and analyzed with Flowjo v9 software.
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Tetramers for Immune Cell Analysis

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Mouse and human CD1d tetramer (TET+) unloaded or loaded with α-galactosylceramide (α-GalCer) analog PBS57 and human MR1 tetramer (TET+) loaded with 6-FP (control) or 5-OP-RU were provided by NIH tetramer facility. Fluorochrome-conjugated antibodies against mouse CD3, CD4, CD8α, CD69, NK1.1, TCRβ, Ly6G, CD11b, B220, CD11c, Ly6C, F4-80, IFN-γ, IL-17A, Vβ2, Vβ7, and Vβ12 and human CD3, CD4, CD8α, Vα7.2, CD161, CD14, and CD19 were purchased from BioLegend. Vβ4, Vβ5.1/5.2, Vβ6, Vβ8.1/8.2, Vβ9, Vβ11, and Vβ13 were purchased from BD. Anti-Vβ10 was purchased from eBioscience. Live dead eFlour506 was purchased from Thermo Fischer Scientific.
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Multicolor Flow Cytometry Analysis

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Muscle leukocyte suspensions were incubated with anti-CD16/CD32 (anti-mouse, clone 2.4G2; BD) to block binding to Fc receptors before staining. The following mouse mAbs used for staining were all obtained from BD: CD3e (hamster anti-mouse, clone 145-2C11), Vβ8.1/8.2 (mouse anti-mouse, clone MR5-2), NK1.1 (mouse anti-mouse, clone PK136), and pan-NK (rat anti-mouse, clone DX5). Antibodies were conjugated to FITC, PE, and/or Cy5. The following antibodies were biotinylated and revealed with Tricolor-conjugated streptavidin (Ebioscience): anti–asialo-GM1 (CL8955; Cedarlane Laboratories) or rabbit sera (control; Invitrogen). Optimal working dilutions were determined for each antibody before use. All incubations were performed in Ca+,Mg+-free Dulbecco’s PBS (Invitrogen) at 4°C for 30 min. After the last wash, 103 live cells per sample were acquired on a FACScalibur (Becton Dickinson) and analyzed with CELL Quest Pro software (Becton Dickinson). CD1d tetramers were obtained from the National Institutes of Health Tetramer Core Facility.
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