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379 protocols using live dead aqua

1

Phenotyping Malaria-Specific CD8+ T Cells

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Lung-resident leukocytes were first stained with Live/Dead Aqua (Life Technologies, USA), and then incubated with PE-labeled SQLLNAKYL-H-2Db (Pb1) tetramer for 15 min on ice. The cells were then incubated on ice for 30 min with anti-CD8 mAb coupled to BV605 (Biolegend, USA) and anti-CD16/32 coupled to APC-Cy7 (Biolegend, USA). Next, the cells were washed and fixed in 1% PFA for 20 min. For intracellular staining, cells were incubated with 10 µg/ml Brefeldin A (eBioscience) in 1 ml RPMI media at 37 °C for 3 h. The live cells were determined by staining with Live/Dead Aqua for 30 min followed by surface staining with PE-labeled SQLLNAKYL-H-2Db (Pb1) tetramer for 15 min. The samples were then fixed in 1% PFA overnight at 4 °C. The following day, the cells were permeabilized with 0.5% w/v Saponin (Sigma Aldrich) and intracellular stained (antibodies listed in Supplementary Table 2) on ice. The cells were then washed and re-suspended in FACS buffer before acquisition on a Fortessa cytometer (Becton Dickinson) and analysis with FlowJo software v. 10.0 (Tree Star).
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2

Multiparameter flow cytometry analysis of T cell activation and B cell HLA-DR expression

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For analyzing DR2a and DR2b expression levels on B cells and monocytes, PBMCs from HLA-DR15+ donors were incubated with human IgG (Sigma-Aldrich) to block unspecific antibody binding to Fc-receptors, labeled with Live/Dead® Aqua (Invitrogen), and then stained for surface marker using fluorochrome-conjugated antibodies, including Alexa Fluor 488-conjugated anti-DR2a antibody (5 μg/ml, One Lambda, Thermo Fisher Scientific) and Alexa Fluor 647-conjugated anti-DR2b antibody (5 μg/ml, One Lambda, Thermo Fisher Scientific), at 4°C. For analyzing CD69, CD25, and TCR α/β expression on TCCs after stimulation, TCCs were harvested at different time points after stimulating with peptides and washed twice with PBS. TCCs were then incubated with human IgG (Sigma-Aldrich), labeled with Live/Dead® Aqua (Invitrogen), and stained for surface marker using fluorochrome-conjugated antibodies, including anti-human CD69 antibody, anti-human CD25 antibody, anti-human TCR α/β antibody, anti-human CD4 antibody, and anti-human CD3 antibody (Biolegend; Key Resources Table), at 4°C. Cells were washed twice after staining and resuspended with cold PBS containing 2mM ethylenediamine tetraacetic acid (EDTA, AppliChem) and 2% FCS (Eurobio). Measurement was performed using LSR Fortessa Flow Cytometer (BD Biosciences) and data were analyzed using FlowJo (Tree Star).
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3

Canine Immune Cell Characterization

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Cryopreserved PBMCs were recovered for FACS analysis and were pretreated by blocking in blocking buffer (1% FBS/PBS) with Human TruStain FcX Fc receptor blocking solution (BioLegend) per 1,000,000 cells. Cells were stained with the following fluorochrome-tagged antibodies, which have been validated to be specific or cross-reactive to canine immune cell epitopes, using manufacturer’s recommendations: (1) T and B cell panel: CD44-FITC (BioRad, YKIX337.78), CD5-PE (BioRad, YKIX322.3), CD79α-PerCP Cy5.5 (Invitrogen, clone HM47), CD4-PE Cy7 (BioRad, YKIX302.9), CD11b-PE CF594 (BioLegend, clone M1/70)[27 (link),28 ], CD21-AF647 (BioRad, CA2.1D6), CD45RA (BioRad, clone CA4.1D3), goat anti-mouse IgG APC Cy7 (BioLegend), CD8α AF700 (BioRad, clone YCATE55.9), CCR7 (BD, clone 150503)[29 (link)], C45RA (BioRad, clone CA4.1D3), and Live/Dead Aqua (Invitrogen); and (2) T cell function panel: CD107β-FITC (BioRad, clone AC17), IL-4 PE (BioRad, clone CC02), CD4-PE Cy7 (BioRad, clone YKIX302.9), TNFα-PE CF594 (BioLegend, clone MaB11)[30 (link)], IFNγ-AF647 (BioRad, clone CC302), CD8α-AF700 (BioRad, clone YCATE55.9), Granzyme B-Pacific Blue (BioLegend, clone GB11)[31 (link)], and Live/Dead Aqua (Invitrogen). Cells were acquired on an LSR II. Flow cytometry gating was determined using cells stained with secondary only & single-color controls, and data were analyzed using FlowJo 10.
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4

Canine Immune Cell Characterization

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Cryopreserved PBMCs were recovered for FACS analysis and were pretreated by blocking in blocking buffer (1% FBS/PBS) with Human TruStain FcX Fc receptor blocking solution (BioLegend) per 1,000,000 cells. Cells were stained with the following fluorochrome-tagged antibodies, which have been validated to be specific or cross-reactive to canine immune cell epitopes, using manufacturer’s recommendations: (1) T and B cell panel: CD44-FITC (BioRad, YKIX337.78), CD5-PE (BioRad, YKIX322.3), CD79α-PerCP Cy5.5 (Invitrogen, clone HM47), CD4-PE Cy7 (BioRad, YKIX302.9), CD11b-PE CF594 (BioLegend, clone M1/70)[27 (link),28 ], CD21-AF647 (BioRad, CA2.1D6), CD45RA (BioRad, clone CA4.1D3), goat anti-mouse IgG APC Cy7 (BioLegend), CD8α AF700 (BioRad, clone YCATE55.9), CCR7 (BD, clone 150503)[29 (link)], C45RA (BioRad, clone CA4.1D3), and Live/Dead Aqua (Invitrogen); and (2) T cell function panel: CD107β-FITC (BioRad, clone AC17), IL-4 PE (BioRad, clone CC02), CD4-PE Cy7 (BioRad, clone YKIX302.9), TNFα-PE CF594 (BioLegend, clone MaB11)[30 (link)], IFNγ-AF647 (BioRad, clone CC302), CD8α-AF700 (BioRad, clone YCATE55.9), Granzyme B-Pacific Blue (BioLegend, clone GB11)[31 (link)], and Live/Dead Aqua (Invitrogen). Cells were acquired on an LSR II. Flow cytometry gating was determined using cells stained with secondary only & single-color controls, and data were analyzed using FlowJo 10.
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5

Single Cell Isolation and Staining

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Spleens were manually disrupted by passing through a 70 uM cell strainer to generate a single cell suspension. Cells were resuspended in PBS then stained with the amine-reactive dye Live/Dead Aqua (Invitrogen) for 20 minutes. Surface staining was performed with antibody cocktails using antibodies for Ly108 (13G3, BD), CX3CR1 (SA11F11, Biolegend), CD4 (RM4–5 BD and Biolegend), CD44 (IM7, Biolegend, BD, or Invitrogen), CD8 (53–6.7, BD), KLRG1 (2F1, Biolegend), CD101 (Moushi101, eBioscience), TCRbeta (H57–597, Biolegend), NKG2A (16A11, Biolegend), CD94 (18d3, Biolegend), CD45.2 (104, Biolegend), and CD45.1 (A20, Invitrogen). Tetramer specific for H2-Db-restricted to the gp33–41 epitope of LCMV was obtained from the National Institutes of Health Tetramer Core Facility. Surface staining was completed in staining buffer of 1:1 Brilliant Stain (BD) and 2% FBS in PBS with 5% Fc block (2.4G) and stained for 1 hour at 4 degrees. Cells were washed and fixed in 4% paraformaldehyde for flow cytometric analysis on a BD Fortessa Flow Cytometer. Data were analyzed using FlowJo software (TreeStar, version 10.8.0). For all analysis, doublets were excluded. Cells were gated on live events using Live/Dead Aqua (Invitrogen). For scRNA-sequencing and scTCR-sequencing, cells were sorted on a BD FACSAria II cell sorter as previously described 16 .
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6

Multiparameter Flow Cytometry of Immune Cells

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Single cell suspensions from mouse experiments were stained with Live/dead Aqua (Molecular Probes, Inc.), CD4-PerCP, CD8-Pacific Blue, CD69-BV605, CD62E-PE, CD62E-BV421, CD62P-Alexa647, CD162-AlexaFlour647, HECA454-PE (BD Bioscience), CD25-APC, CD31-BV605, CD105-Pacblue, I/A-I/E-BV421, CD45-APCCy7, EpCAM-APC-Cy7, Podoplanin-PE, CD31-PECy7, EpCAM-FITC, CD64-BV711 (Biolegend), CD11c-PECy5.5 (Invitrogen) CXCR3-PECy7, CD3-Alexa700 and Ly6C-efluor450 (eBioscience). For subsequent detection of CXCL10 mRNA Primeflow® RNA Assay (eBioscience) was used accordingly to manufacture protocol. Samples were acquired on an LSR-II flow cytometer (BD Biosciences) and analysed using FlowJo software (Tree Star Inc.).
Single cell suspension isolated from human tumors and unaffected colon tissue were stained with Live/dead Aqua (Molecular Probes, Inc.), CD31-Alexa700, (Biolegend), CD4-PerCP, CD8-BV711, CD105-APC, CD14-Alexa700, CD19-APCH7 and CD19-PE-CF594 (BD bioscience) followed by permeabilization with Fix & Perm kit (ADG Bio research GMBH) and staining with CXCL9-FITC (R&D) and CXCL10-PE (Biolegend), flow cytometry analyses were performed as above.
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Comprehensive Immune Profiling of Syngeneic Tumors

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Syngeneic tumors were dissociated to single cells, counted, normalized, and stained for viability (Fixable Viability Dye or Live/Dead Aqua, Thermo Fisher Scientific; Supplementary Table S4). Peripheral blood and spleen cells were stained with Zombie NIR viability dye or Live/Dead Aqua (Thermo Fisher Scientific). Tumor and spleen cells were blocked with TruStain FcX (anti-mouse CD16/32, BioLegend) prior to fluorescent antibody staining (antibodies detailed in Supplementary Table S4). Tumor samples were run on an LSRFortessa or FACSymphony (BD Biosciences) with 123count eBeads (Thermo Fisher Scientific). Peripheral blood and spleen samples were run on an Attune NXT flow cytometer or FACSymphony (BD Biosciences). All analyses were carried out using FlowJo V10 (TreeStar).
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Multiparametric Flow Cytometry of PBMCs

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PBMCs were stimulated for 8 hours in the presence of 1x brefeldin A (eBioscience) as described earlier. Cells were washed and stained with viability dye (Live/Dead Aqua, Life Technologies), followed by staining of extracellular surface markers with fluorescently conjugated antibodies specific for CD14, CD4, CD8, CD19, and CD56 (BD Biosciences). After washing, the cells were fixed and permeabilized with the Foxp3 / Transcription Factor Staining Buffer Set (eBioscience) according to the manufacturer’s recommendations. Intracellular staining was subsequently performed for IL-2, IFN-γ, and TNF-α with specific antibodies (all from BD Biosciences). Cells were washed again and immediately analyzed on a BD LSR Fortessa HTS flow cytometer. Data were then analyzed with FlowJo v7.6.5 or vX software (Tree Star).
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9

Flow Cytometry Analysis of MAIT and NK Cells

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PBMC were thawed, and washed with RPMI 1640 supplemented with 10% fetal calf serum (Lonza, Walkersville, MD, USA). For flowcytometry, 500 000 viable PBMC were stained with anti‐CD8‐FITC(RPA‐T8); anti‐CD3‐Amcyan(SK7); anti‐CD161‐eFluor450(HP‐3G10); Anti‐TCR Vα7.2‐PE(3C10); anti‐CD56‐APC(N901); anti‐CD56‐APC‐eFluor780(CMSSB); anti‐CD38‐PerCp‐eFluor710(HB7); or anti‐HLA‐DR‐PerCP‐Cyanine5.5(LN3) for 20 minutes at 4°C. Marker expression was detected by flowcytometry (MACSQuant Analyser 10 [Miltenyi Biotec, Cologne, Belgium]). MAIT‐cells were defined as CD3+CD161+Vα7.2+ cells within the lymphocyte gate and NK‐cells were defined as CD3CD56+ cells within the lymphocyte gate.
Liver aspirates and paired blood were stained with anti‐CD3‐Alexa‐Fluor700(OKT‐3); anti‐CD56‐APC‐eFluor780(CMSSB); anti‐CD45‐PE‐eFluor610(HI30); anti‐CD235a‐FITC(HIR2) or anti‐CD4‐FITC(13B8.2); anti‐CD3‐eVolve605(RPA‐T8); anti‐TCR Vα7.2‐PE(3C10); anti‐CD161‐eFluor450(HP‐3G10); and Live/Dead Aqua (Life Technologies, Carlsbad, CA, USA). Cells were analysed using a FACS ARIA cell sorter (BD‐Biosciences), San Jose, CA, USA and MACSQuant Analyser 10. All antibodies were purchased from eBioscience (San Diego, CA, USA), Beckman (Brae, CA, USA) or Biolegend (London, UK).
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10

Multiparameter Flow Cytometry of Immune Cells

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CD45.2-V500 and TNFα-APC-Cy7 were purchased from BD Biosciences (San Jose, California). KLRG1-FITC, Eomes-PE, CD107a-PE, CD107b-PE, CD27-PE, CD127-PE-Cy5, CD127-PerCP-Cy5.5, Tbet-PerCP-Cy5.5, IFNγ-PerCP-Cy5.5, Eomes-PErCP-efluor710, CD45.1-PECy7, KLRG1-PE-Cy7, Tbet-PE-Cy7, IRF4-AlexaFluor647, CD44-AlexaFluor700, CD62L-APC-eFluor780, CD44-eFluor450, KLRG1-eFluor450, IFNγ-eFluor450, CD90.2-APC-eFluor780, CD45.1-APC-eFluor780, IL-2-PerCP-Cy5.5 were purchased from eBioscience (San Deigo, California). CD8-PE-TexasRed, GranzymeB-PE, GranzymeB-APC, Live-Dead-Violet, Live-Dead-Aqua and goat-anti-rabbit IgG-AlexaFluor647 and -AlexaFluor488 were purchased from Life Technologies (Grand Island, New York). H2Db-GP33 monomers were prepared at UMMS; LCMV-specific (H2Db-NP396, H2Db-GP276) and Influenza A PR8-OVAI-specific (H2Kb-OVA257) monomers were obtained from the NIH Tetramer Core Facility (Atlanta, Georgia). Intracellular TCF1 staining was performed using rabbit-anti-mouse TCF1 (Cell Signaling Technology, Danvers, Massachusetts) followed by staining with goat-anti-rabbit secondary (Life Technologies). Samples were analyzed on an LSRII flow cytometer (Becton Dickinson), and data were analyzed using FlowJo (Tree Star).
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