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16 protocols using human truestain fcx

1

Flow Cytometry Analysis of Dendritic Cells

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A total of 105 cells were incubated with a flow cytometry media (PBS w/o Ca2+ or Mg2+ with 0.01% sodium azide and 1% fetal bovine serum) enriched with human TrueStainFcX™ (BioLegend, San Diego, CA, USA) for 15 min at 4°C in the dark. Cells were then incubated with the antibodies for 30 min at 4°C in the dark, with additional mixing at 15 min. Cells were washed twice in FACS media and re-suspended in 100 µl of 1% FlowFix (Polysciences, Warrington, PA, USA). The following antibodies were employed: CD1a (HI149; BioLegend, San Diego, CA, USA), CD14 (Tuk4; Invitrogen, Grand Island, NY, USA), CD83 (HB15e; BD, San Jose, CA, USA), CD115 (AFS98; BioLegend, San Diego, CA, USA), CD124 (G077F6; BioLegend, San Diego, CA, USA), and CD126 (UV4; BioLegend, San Diego, CA, USA).
The frequency of naturally occurring DC was analyzed with a BDCA enumeration kit (Myltenyi Biotec, Germany) (15 (link), 28 (link)). Enumeration protocol takes into account leukocytes count in the blood.
Cells were analyzed with an LSR™ (BD, San Jose, CA, USA) or a FACSCalibur™ (BD, San Jose, CA, USA). Non-specific antibodies were used as a negative control. At least 10 × 104 were collected. Data were expressed as a frequency of cells while mean fluorescent intensity (MFI) was a measure of receptor density. MFI is presented as relative to non-specific binding after exposing cells to non-specific antibodies.
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2

Monocyte Subset Identification Protocol

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For classification viable monocyte singlets were classified into their respective subsets based upon expression of HLA-DR, CCR2, CD14, and CD16 (See Fig 1). 50 μL of blood was treated first with Human True Stain FcX and True Stain Monocyte Blocker (Biolegend) for 10 minutes, labeled with fluorescent antibodies for 30 min, followed by red blood cell removal with lysis buffer (Biolegend). Data were acquired on an Attune NxT flow cytometer within 2 hrs of blood collection.
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3

Detecting MICA/B on Tumor Cells

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1 × 105 tumor cells per well were cultured in 96-well plates (flat bottom plate for adherent cells, round bottom plate for suspension cells) at 37 °C 5% CO2. 7C6 (a human IgG1 mAb kindly provided by Dr Kai W. Wucherpfennig) or human IgG1 isotype control (Biolegend, Koblenz, Germany) antibody were added at 10 µg/mL. After 24 h of culture, MICA and MICB on cell surface were detected following staining with APC conjugated anti-MICA/B antibody or IgG2a isotype control. For detaching adherent cells without disturbing the integrity of surface molecule, Accutase (Biolegend, Koblenz, Germany) was used. Prior to the staining process, Fc receptors were blocked with Human TrueStain FcX™ (Biolegend, Koblenz, Germany) at a final dilution of 1:100. Hoechst 33258 (Cayman Chemical, Hamburg, Germany) was added before flow cytometry analysis for viable cells gating. Samples were acquired using FACS Canto II (BD).
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4

AXL and MERTK Expression in Immune Cells

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Cells were blocked with Human TrueStain FcX and TrueStain Monocyte Blocker (Biolegend) and stained with the following antibodies: anti-AXL clone #108724 and anti-MERTK clone #125518 (R&D Systems). Appropriate forward and side scatter profiles were used to exclude debris and doublets from the analysis. Dead cells were excluded based on LIVE/DEADTM Fixable Aqua (Thermo Fisher Scientific) staining. Readings were done on an AttuneTM Nxt Flow Cytometer and analysed/visualized using FlowJoTM software.
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5

GD2 Surface Staining in Neuroblastoma Cells

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Surface staining for GD2 was performed on SH-SY5Y-Fluc, CHLA-136-Fluc, CHLA-255-Fluc and COG-N-415× cells. Briefly, cells were washed twice in fluorescence-activated cell sorting (FACS) buffer (PBS with 5% bovine serum albumin (Fisher Scientific SH3057402) and centrifuged for 8 minutes at 100 × g. Fc-receptors were blocked by incubation in human Fc-blocker for 10 min at 4°C (Human True Stain FcX, Biolegend 422302), followed by incubation with anti-human GD2 antibody (BioLegend 357306) and isotype-matched irrelevant control (BD Pharmingen 340754) for 1 hr in the dark at 4°C. Cells were then washed twice in FACS buffer, and DAPI was added (0.5 ng/ml final concentration) to each tube. Flow cytometry was conducted using a LSR II flow cytometer (BD Biosciences), and BD FACSDiva™ software was used to collect and analyze data. Experiments were repeated a minimum of three times. Ratios for median fluorescence intensity (MFI) index were calculated as follows: (MFI of viable cells stained with specific antibody / MFI of viable cells stained with isotype-matched irrelevant antibody).
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6

Multiparametric Immune Cell Profiling

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0.5 to 1.0 × 106 cells from each sample were aliquoted into 5ml round bottom tubes or 96-well U-bottom plates for antibody staining. Cells were washed with PBS and stained for viability using Zombie NIR Fixable Viability stain (1:2500, BioLegend 423106) in PBS for 20 min at room temperature in dark. Cells were washed with FACS buffer, blocked with Human TrueStain FcX (1:200, Biolegend 422302), and stained with the surface antibody cocktail in FACS buffer for 30 min at 4C in dark. All antibodies and dilutions used for staining are listed in Table S1 and Table S2.
For intracellular staining, cells were fixed and permeabilized using the Foxp3/Transcription Factor Staining Buffer Set (eBioscience 00-5523-00). To block non-specific binding, 10ul of FBS was added to the cells in the residual volume of perm buffer and incubated for 5 min. Without washing, the intracellular antibody cocktail was added to the cells and stained for overnight at 4C. After the staining, the cells were washed twice with perm buffer, once with FACS buffer, and resuspended in FACS buffer for analysis. Antibody-stained cells were analyzed on an Aurora (Cytek) and the data analysis was performed using FlowJo (BD). Dimensionality reduction and hierarchical clustering analyses were performed using R functions and packages including ComplexHeatmap.
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7

Tumor Immune Cell Profiling

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Tumor tissues were digested using Mouse Tumor Dissociation kits (Miltenyi) according to the manufacturer’s protocols. Isolated cells were stained for viability using the Aqua Amine fixable live dead dye (Thermo Fisher) at room temperature using standard protocols. After viability staining, cells were resuspended in FACS buffer (PBS with 0.5% BSA and 2 mM EDTA) and Fc blocked using human TrueStain FcX (Biolegend). For cell surface staining, cells were incubated for 30 minutes at 4C with the following anti-mouse antibodies from Biolegend CD4-FITC, clone GK1.5, CD8a-BV786, clone 53–6.7; CD3e-Percp-Cy5.5, clone 17A2; and ThermoFisher CD45-AlexaFluor 700, clone 30-F11. Cells were then washed twice, fixed, and permeabilized (eBiosciences Intracellular Fixation & Permeabilization Buffer Set) prior to intracellular staining with FOXP3-PE, clone 150D. Samples were analyzed using an Attune NxT flow cytometer (Thermo Fisher) and data was analyzed using FlowJo 10 (TreeStar).
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8

Multiparameter Analysis of NK and T Cells

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For high parameter analysis using a multiparameter NK and T cell panel, 5 × 106 PBMCs were stained in 96-well v-bottom plates using an optimized antibody panel, as described in Supplemental Table 2. Briefly, cells were washed with PBS, resuspended in 1 ml viability dye, and incubated at room temperature in the dark for 10 minutes. Cells were washed once with cold FACS buffer (PBS with 2% heat-inactivated FCS and 2 mM EDTA); resuspended in a staining cocktail that included the anti-γδ TCR antibody, human TrueStain FcX (BioLegend, 422302), and mouse serum (Jackson ImmunoResearch Labs, 015-000-001); and then incubated on ice for 10 minutes. Antibodies in the panel were sequentially added with 50 μl Horizon Brilliant Stain buffer (BD Bioscience, 56379) and then incubated on ice for 25 minutes. After washed with FACS buffer, samples were fixed in 100 μl Fluorofix Buffer (BioLegend, 422101). Samples were analyzed on a LSRFortessa X50 (FACSymphony) cytometer (BD Bioscience). Data were analyzed with FlowJo 10.7.1. NK and CD8+ T cells were gated as shown in Supplemental Figures 5 and 6, respectively.
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9

Bone Marrow Mononuclear Cell Isolation

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Frozen human Bone Marrow Mononuclear Cells (BMMCs, Allcells) were thawed in a 37 °C water bath for 1 min and transferred to a 15 mL centrifuge tube. 10 mL of pre-warmed DMEM with 10% FBS was added to cells drop-wisely. The cells were spun at 400g for 3 min at room temperature. After removing supernatant, the cells were washed twice in 0.5 mL PBS with 0.04% BSA. To deplete neutrophils, the cells were resuspended in 100 μl chilled DPBS with 0.2% BSA and 10 μl of human TrueStain FcX (BioLegend, 422302) and incubated on ice for 10 min to reduce non-specific labeling. The cells were then incubated on ice for another 30 min after adding 0.5 μl of biotin anti-human CD15 antibody (BioLegend, 301913). After immunostaining, 25 μl of MyOne T1 beads were added to the sample to capture the neutrophils for 5 min at room temperature. We then added 900 μl of DPBS with 0.2% BSA to dilute the sample. The sample was placed on a magnet for 3 min and 1 ml of the sample was transferred to a new tube while the sample was on the magnet. The cells were ready for fixation and SHARE-seq experiment.
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10

Characterization of Cultured B Cells

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Cultured B cells were characterised by flow cytometry on BD LSR Fortessa II with Live/Dead staining with Zombie NIR Dye (Biolegend), Fc blocking using Human Truestain FcX (Biolegend) and incubation with antibodies listed in online supplemental table 1). Samples undergoing plasmablast differentiation were cell sorted on BD FACSAria II into IgD+CD27- naïve B cells and CD20lowCD27+CD38+ plasmablasts. Immediately after sorting, cells were resuspended in RNAprotect Cell Reagent (QIAGEN) and frozen at −80°C for RNA extraction. Data were analysed using Flowjo software V10.
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