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5 protocols using cd56 pe cy5

1

Quantifying Immune Cell Subsets

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For cell phenotype analysis, monoclonal antibodies were directly added to 100 μL aliquots of heparinized whole blood and incubated at room temperature for 15 min. The antibodies used were: CD3 PECy7, CD14 APC, CD56 PE-Cy5 and CD19 PerCp (Biolegend, San Diego, CA, USA), CD4 Viogreen (Miltenyi Biotec GmBh, Bergisch Gladbach, Germany), CD39 Fitc, CD73 PE, CD25 BV421 and CD127 AlexaFluor 647 (BD Biosciences, San Jose, CA, USA). Red blood cells were lysed and white cells were fixed using BD FACS lysing solution (BD Bioscience). Negative populations were determined using respective anti-human isotype controls. Samples were acquired using a MACSQuant Analyzer 10 flow cytometer (Miltenyi Biotec GmBh) and the data were analyzed using FlowJo software v. 10.0 (TreeStar Inc., Ashland, OR, USA).
We compared the frequencies of four subsets based on CD39 and CD73 expression (CD39CD73+, CD39+CD73+, CD39+CD73, and CD39CD73) within each studied population (B cells as CD3CD19+, CD4+ T cells as CD3+CD4+, CD8+ T cells as CD3+CD4, NK cells as CD3CD4CD19CD56+, Tregs as CD3+CD4+CD25++CD127, and monocytes as CD14+). The percentage of these four subsets was related to their corresponding precursor populations (CD4+ T, CD8+ T, B, NK, and monocytes). In the case of Treg, the percentage was related to CD4+ T cells.
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2

Multiparametric Flow Cytometry Analysis of Natural Killer Cells

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MNCs were stained with labeled antibodies, CD3 ECD (Biolegend), CD45 Krome Orange (R&D systems), CD56 PE-Cy5 (Biolegend), CD16 APC-Cy7 (Biologend), CD326 PerCPCy5.5 (Biolegend). Phenotypic analysis was performed using DNAM-1 FITC (Becton Dickinson), 2B4 FITC (Biolegend), NKG2A APC (Beckman Coulter), NKG2D APC (Biolegend), NKp30 PE (Biolegend) and NKp46 PE(Biolegend), isotype controls for IgG1 and IgG2a, (all Biolegend). Dead cells were stained with 1:1000 diluted sytox blue (Life Technologies; Invitrogen). Flow cytometry analysis was performed on a Gallios flow cytometer from Beckman Coulter. Analysis was done in Kaluza 1.5 (Beckman Coulter). Gating strategy is shown in Supplementary Figure 1.
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3

Intracellular Cytokine Staining Protocol

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For intracellular staining, brefeldin A was added to the cells and incubated for 4 hours. The cells were placed on ice, harvested, and stained for surface markers for 30 minutes at 4°C in FACS buffer (PBS + 0.5% BSA and 2 mM EDTA). After washing (FACS buffer) the cells were fixed and permeabilized (BD FACS lysing and permeabilization solution 2, BD Biosciences) for 10 minutes. Cells were washed and incubated (30 minutes, 4°C) with antibodies for intracellular staining, washed and acquired using the BD Fortessa X-20 system, and analyzed using FlowJo software (version 10, BD).
The following antibodies were used for flow cytometry: CD16-BV421, CD56-PE-Cy5, CD3-Pacific Blue, CD4-BV786, CD8-AF700, CD161-BV605, and vα7.2-PE-Cy7 from BioLegend; IFN-γ-PE, IP-10-PE, and granzyme B–AF647 from BD Biosciences; and interleukin 15 (IL-15)–APC from Invitrogen.
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4

Characterizing NK and B Cell Responses

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NK and B cells were isolated from uninfected participant PBMCs (Stemcell Technologies), plated in BCM (RPMI 1640 with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin) with or without CD16 mIgG-blocking antibody (BioLegend, catalog no. 302001, 1 μg ml−1), and incubated at 37 °C for 1 h. The cells were washed in phosphate-buffered saline (PBS) and stained with scDbs (at indicated concentrations, in PBS) at 4 °C for 1 h. The cells were washed and stained with the following antibodies (1:50 dilution)/dye (1:1,000 dilution) at 4 °C for 45 min: CD3-BV605, CD19-BV421, CD56-PE/Cy5 (BioLegend, catalog nos. 317321, 302233 and 304607, respectively), 6× His tag-AF488 and Fixable Viability Dye-eFluor780 (Thermo Fisher Scientific, catalog nos, MA1-135-A488 and 65-0865-14, respectively). The cells were washed, and samples were acquired on an Intellicyt iQue Screener Plus (Sartorius). Data were analyzed with FlowJo (BD Bioscience; see Supplementary Fig. 4 for gating example). NK cells were defined as live CD3CD19CD56+ lymphocytes, T cells as live CD3+ lymphocytes and B cells as live CD19+ lymphocytes. All conditions were tested in triplicate, mean and s.d. shown.
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5

Comprehensive Bone Marrow Cell Immunophenotyping

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The detailed protocol for whole BM staining has been previously reported (Basso-Ricci et al., 2017 (link)). In brief, Precision Count beads (BioLegend) were added to 100 μl of P1 BM sample to allow absolute quantification of hematopoietic cell subsets, and red blood cell lysis was performed. The lysed sample was labeled with fluorescent antibodies for CD3-BV605, CD56-PE-Cy5, CD14-BV510, CD61/41-PE-Cy7, CD135-PE, CD34-BV421, CD45RA-APC-Cy7 (BioLegend), CD33-BB515, CD66b-BB515, CD38-BUV737, CD45-BUV395, CD90-APC, CD10-BV786, CD11c-BV650, CD19-APCR700, CD7-PE-Cy5.5, and CD71-BV711 (BD Biosciences). Titration assays were performed to assess the best antibody concentration. After surface marking, the cells were incubated with PI (BioLegend) to stain dead cells. All samples were acquired using a BD LSR Fortessa (BD Bioscience) flow cytometer after calibration with SPHERO rainbow calibration particles (Spherotech), and raw data were collected using BD FACSDIVA software. The data were subsequently analyzed with FlowJo software, and the graphical output was automatically generated using GraphPad Prism.
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