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3 protocols using permeabilization buffer 10x

1

Multiparametric Flow Cytometry for DC Subsets

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For DCs flow cytometry, PBMCs were centrifuged, pelleted and washed with Phosphate-buffered saline (PBS) and stained for 35 min at room temperature with LIVE/DEAD Fixable Aqua Dead Cell Stain (Life Technologies), BV421 CD86, BV650 CD11c, BV711 HLA-DR, BV786 CCR7 (CD197), FITC Lin-2 (CD3, CD14, CD19, CD20, CD56), BV605 CD16, PeCF594 PD-L1 (CD274), APC Integrin-β7 (BD Biosciences), PerCPCy5,5 CD4, APCCy7 CD1c, PeCy7 CD141 (BioLegend) and AF700 CD123 (R&D, San Diego, CA) antibodies. Then PBMCs were washed with Permeabilization Buffer 10X diluted 1:10 (eBioscience™), permeabilized by Fixation/Perm buffer (eBioscience™), and intracellularly stained with PE IDO (eBioscience, San Diego, CA, USA) antibody. DCs were gated based on Lin-2 HLA-DR expression. Each subset (mDCs and pDCS) was gated based on CD123 and CD11c expression. mDCs subsets were gated by using CD16, CD1c and CD141 staining, for gating strategy see Supplementary Fig. 1. Flow cytometry analyses were performed on an LRS Fortessa flow cytometer using FACS Diva software (BD Biosciences). Data were analyzed using the FlowJo software (Treestar, Ashland, OR). At least 1 × 106 events were acquired per sample.
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2

Flow Cytometry Analysis of Mouse and Human T Cells

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Anti-human CD3e-V500, CD4-APC-H7, CD8-APC-H7, CD25-PE, CD39-PE (clone TU66), CD73-APC (clone AD2), PD1-PE-Cy7 (clone EH12.1), and CD127-PerCP-Cy5.5 antibodies were purchased by BD Biosciences (Germany), anti-human FOXP3-FITC antibody was from eBioscience (Germany). Anti-mouse CD3e-PerCP-Cy5.5, -APC, -V500 and -V450; CD4-APC, -BV421, -APC-Cy7 and -APC-H7; CD8a-APC-Cy7, -PE-Cy7 and -APC-H7; CD25-APC, -APC-Cy7 and -V450; CD44-PE; CD45-V500; CD45RB-PE; CD62 L-APC; CD69-APC; CD73-BV605 (clone TY/11.8) and PD1-PerCP-Cy5,5 (clone J43) were purchased by BD Biosciences (Germany). Purified anti-mouse CD3e and CD28, as well as FOXP3-FITC, CD73- eFluor® 450, -PE (clone TY/11.8 for both) and CD39-PE-Cy7, -PE (clone DM24S1 for both) were from eBioscience (Germany). BSA, Trypan blue, PMA, and Ionomycin were obtained from Sigma (Germany). Phosphate buffer saline (PBS), RPMI-1640 with L-glutamine and Penicillin-Streptomycin were purchased by PAA (Germany). Fetal bovine serum (FBS) was from PAN Biotech (Germany). Brefeldin A was purchased by BD Biosciences (Germany). Foxp3/Transcription Factor Staining Buffer Set and Permeabilization Buffer (10X) were obtained from eBioscience (Germany). Red Blood Cell (RBC) Lysis Buffer was from Biolegend (Germany).
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3

Multiparameter Flow Cytometry Protocol

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Single cell suspensions from organs and tissues were stained with optimized antibody dilutions for 15 minutes at 4°C (Supplementary Table S4). Antibodies were directly conjugated to Brilliant Ultraviolet (BUV)395, Brilliant Violet (BV)786, BV711, BV650, BV605, Pacific Blue (PB), fluorescein isothiocyanate (FITC), phycoerythrin (PE), PE-Cy5.5, PE-Texas Red, peridinin-chlorophyll-protein complex (PerCP)-Cy5.5, PE-Cy7, allophycocyanin (APC), APC-Alexa 700, or biotin. Biotinylated antibodies were revealed with Streptavidin APCeFluor780. Cells were resuspended in FACS buffer (1% BSA+0.01% NaN3 in PBS1x, filtered) and incubated with rat plus rabbit serum followed by incubation with antibody cocktail against surface molecules. For intracellular staining, cells were fixed (IC Fixation Buffer, eBioscience) and permeabilized (Permeabilization Buffer 10x, eBioscience). Dead cells were excluded through 4,6 diamidino-2-phenylindole (DAPI) uptake or Aqua live/dead staining. Doublets were excluded through forward scatter–height by forward scatter–width and side scatter–height by side scatter–width parameters. Cells were acquired on a LSR Fortessa SORP (BD Biosciences) and data were analyzed using FlowJo (Tree Star). Cell sorting was performed on a FACSAria II (BD Biosciences), and cell purity after sorting was > 99%.
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