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1

Murine Splenocyte Isolation and Flow Cytometry

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Mice were sacrificed and spleens were removed. The tissues were dissociated, single cell suspensions prepared, and red blood cells were lysed using GEY'S buffer [27 (link)]. The dissociated splenocytes were treated with FC Block (BD Bioscience) and then stained with the following antibodies; CD3, CD4, CD8, CD25, MHCII (clone M5/114.15.1), B220, γδ-TCR (BD Bioscience), and CLIP (15G4, Santa Cruz Biotechnology). For regulatory T cell (Treg) staining we used the eBioscience mouse regulatory T cell staining Kit according to the manufacturer's directions. Live cells were assessed using the Life Technologies LIVE/DEAD® Fixable Aqua Dead Cell Stain Kit according to the manufacturer's directions. Splenocytes were analyzed using a BD FACS Canto II flow cytometer and data were analyzed using FlowJo software (TreeStar Inc.). See Additional file 1: Figure S1 for gating strategy.
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2

Multicolor Flow Cytometry Panel

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Antibodies used include: Ii (In-1, 1:100), H2-M (2E5A, 1:50), Rat IgG1 (R3-34, 1:50; all from BD Biosciences); podoplanin (8.1.1, BioLegend, 1:500); CLIP (15G4, Santa Cruz, 1:5); H2-O (ref. 69 (link); Mags.Ob3, Lisa Denzin, 1:400); 10.1.1 (UVA lymphocyte culture centre, 1:1,000); CD45 (30-F11, 1:1,000), CD31 (390, 1:1,000), MHC-II (M5/114.15.2, 1:50 (Fig. 1) to 1:500 (Fig. 6)), CD8 (53-6.7, 1:1,000), CD4 (GK1.5, 1:1,000), Thy1.1 (HIS51, 1:1,000), Thy1.2 (53-2.1, 1:1,000), CD45.1 (A20, 1:500), CD11c (N418, 1:500), CD11b (M1/70, 1:500), CD69 (H1.2F3, 1:500), CD62L (MEL-14, 1:1,000), CD44 (IM7, 1:1,000), CD25 (PC61.5, 1:500), Y-AE (eBioY-Ae, 1:200), PD-1 (RMP1-30, 1:100), LAG-3 (eBioC9B7W, 1:100), Rat IgG2b (eB149/10H5; all from eBioscience). Intracellular staining for PD-1, LAG-3, Ii, H2-M and H2-O was done using the Cytofix/Cytoperm kit (BD Bioscience), and Ki67 (SolA15, 1:500) and FoxP3 (FJK-16s, 1:100) were stained using Treg permeabilization buffers (eBioscience). Annexin V (1:20) was stained using the eBioscience kit. 4,6-Diamidino-2-phenylindole (DAPI; Sigma) or live/dead aqua (Invitrogen, 1:200) were used to distinguish live cells. Cells were acquired on a FACSCanto II (BD Biosciences) and data analysed using FlowJo (Tree Star).
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