Flow cytometry

For mouse sample flow cytometry analysis, lymphoid cells were obtained and stained with PerCP-Cy5.5 or PE-Cy7 anti-mouse CD8α (53-6.7; BioLegend), BUV395 or BUV737 anti-mouse CD8α (53-6.7; BD Biosciences), PerCP-Cy5.5 or APC anti-mouse CD4 (GK1.5; BioLegend), BV510 or PE-Cy7 anti-mouse CD4 (RM4-5; BioLegend), eFluor450 or PE-Cy7 anti-mouse CD90.2 (53-2.1; BioLegend), PerCP-Cy5.5 anti-mouse CD3ε (145-2 C11; BioLegend), BUV395 anti-mouse CD3ε (145-2 C11; BD Biosciences), Pacific Blue anti-mouse TCRβ (H57-597; BioLegend), APC anti-mouse γδTCR (GL-3; eBioscience), PE mouse CD1d tetramer (NIH Tetramer Core facility), APC anti-mouse/human KLRG-1 (2F1/KLRG1; BioLegend), APC-Cy7, FITC, or PE anti-mouse CD103 (2E7; BioLegend), Alexa Fluor 488, PerCP-Cy5.5 or Pacific Blue anti-mouse CD45.1 (A20; BioLegend), PerCP-Cy5.5, Pacific Blue, or BV510 anti-mouse CD45.2 (104; BioLegend), PE-Cy7 anti-mouse PD1 (RMP 1-30; BioLegend), PE or APC anti-mouse Tim3 (RMT3-23; eBioscience), APC or PE-Cy7 anti-mouse/human CD44 (IM7; BioLegend), Alexa Fluor 488 or PerCP-Cy5.5 anti-mouse CD62L (MEL-14; BioLegend), and PE-Cy7 or APC anti-mouse CD127 (A7R34; eBioscience). Intracellular staining was performed using either the IC/fixation buffer or the Foxp3/Transcription factor staining buffer set (ThermoFisher Scientific), and stained with APC, PE, PerCP-Cy5.5, or PE-Cy7 anti-mouse IFN-γ (XMG1.2; BioLegend), Alexa Fluor 488, APC, or PE anti-mouse IL-17A (TC11-18H10.1; BioLegend or eBioscience), Pacific Blue anti-mouse/human granzyme-B (GB11; BioLegend), PE anti-Ki-67 (SolA15; eBioscience), Alexa Fluor 647 anti-mouse/human TCF-1 (C63D9; Cell Signaling), PE anti-mouse/human TOX (REA473; Miltenyi Biotec) and PE anti-active caspase-3 (C92-605; BD Biosciences). The following antibodies were used for the staining of lymphoid cells isolated from human samples: BV421 anti-CD127 (A019D5; BioLegend), BV711 anti-IL-17A (BL168; BioLegend), BV786 anti-CD4 (SK3; BD Biosciences), FITC anti-IFN-γ (4S.B3; eBioscience), PerCP-Cy5.5 anti-CD3 (UCTH1; BD Biosciences), PE-Cy7 anti-KLRG1 (REA261; Miltenyi Biotec), APC anti-CD103 (Ber-ACT8; BioLegend), Alexa Fluor 700 anti-granzyme-B (GB11; BD Biosciences), and APC-Cy7 anti-CD8 (SK1; BD Biosciences). Human samples were stained using the LIVE/DEAD fixable red dead cell stain kit (Invitrogen) to gate out dead cells. Samples were analyzed with either a FACSVerse, FACSLSR II, LSRFortessa, or FACSAria III (BD Biosciences), and data were analyzed using FlowJo software (TreeStar).