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Zombie uv fixable viability dye

Manufactured by BioLegend
Sourced in United States, United Kingdom

The Zombie UV Fixable Viability Dye is a fluorescent dye that can be used to detect and quantify dead cells in flow cytometry applications. The dye is membrane-impermeable in live cells but penetrates the membranes of dead cells, where it binds to cellular proteins, emitting a fluorescent signal that can be detected using a flow cytometer.

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21 protocols using zombie uv fixable viability dye

1

Purification and Characterization of Mature CD8+ T Cells

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Mature CD8SP cells from PSC-ATOs were isolated by magnetic negative selection using the CD8+ T Cell Isolation Kit
(Miltenyi, Cat. 130–096-495) and sorted by FACS to further deplete CD45RO+ cells (containing immature CD8SP T cells and
DN/4ISP T cell precursors). Purified T cell populations were plated in 96-well U-bottom plates in 200 µl AIM V
(ThermoFisher Scientific, Grand Island, NY) with 5% human AB serum (Gemini Bio-Products, West Sacramento, CA).
PMA/ionomycin/protein transport inhibitor cocktail or control protein transport inhibitor cocktail (eBioscience, San Diego,
CA) were added to each well and incubated for 6h. Cells were washed and stained for CD3, CD4, and CD8 (Biolegend, San Diego,
CA) and Zombie UV™ Fixable Viability dye (Biolegend, San Diego, CA) prior to fixation and permeabilization with an
intracellular staining buffer kit (eBioscience, San Diego, CA) and intracellular staining with antibodies against IFNγ,
TNFα, and IL-2 (Biolegend, San Diego, CA).
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2

Treg-mediated Suppression of T-cell Proliferation

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Tresp cells were thawed, labeled with proliferation dye eFluor670 (eBioscience), stimulated with anti-CD3/CD28 Dynabeads and cultured (2 × 104 cells/well) in a round-bottomed 96-well plate in the presence or absence of each autologous Treg subset (rTreg, aTreg and nonTreg) separately at a 1:1 ratio. After 3 days of culture, cells were harvested, washed and stained with Zombie UV Fixable Viability dye (Biolegend) and analyzed on an LSR-II (Becton & Dickinson). Dead cells were excluded and Tresp cell proliferation was determined by following eFluor670 dilution using FCS-expressTM 6 software (De Novo Software, Glendale, CA). The percentage suppression of proliferation was calculated as follows: %Suppression=%proliferationTrespalone%proliferationTrespincoculturewithTreg%proliferationTrespalone×100%
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3

Purification and Stimulation of T Cells

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CD4+ T cells or CD8+ T cells were purified from PBMCs using magnetic positive selection with biotin human anti-CD4 or anti- CD8 antibodies, respectively, followed by incubation with streptavidin-coupled magnetic microbeads (BioLegend) and positive selection with magnets. Purity was assessed by flow cytometry on a BD LSRFortessa using anti-CD4 (RPA-T4, 1:400) antibodies and anti-CD8 (RPA-T8, 1:400) antibodies. Cells were plated on 48-well plates, coated with anti-CD3 (1 μg ml1) and anti-CD28 (10 μg ml ) antibodies, in RPMI medium or DMEM, supplemented with 10% FCS, penicillin, streptomycin, HEPES, glutamine, pyruvate, nonessential amino acids and β-mercaptoethanol diluted with PBS (1:1), in the presence of IL-2 (10 ng ml1, Peprotech) and IL-12 (10 ng ml1, Peprotech) (TH1 conditions), with or without amino acids. Human CD4+ T cell cultures were supplemented on days 0, 1 and 2 with 5 mM NaCl or 5 mM BHB and collected after 6 days of culture. Cultured cells were stimulated for 6 h with PMA (50 ng ml1) (BioGems) and ionomycin (1 µg ml1) (BioGems) in the presence of brefeldin A (1 μg ml1) (GolgiPlug, BD Biosciences), stained for viability (Zombie UV Fixable Viability Dye (BioLegend)) and surface markers, fixed and permeabilized with 3.7% formaldehyde (Sigma) and 0.1% NP-40, respectively, and stained for intracellular cytokines.
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4

Murine T Cell Polarization Under BHB

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Naive CD4+ T cells or CD8+ T cells were purified from mouse spleens using the magnetic negative selection kit (Mojosort mouse CD4 naive T cell isolation kit, BioLegend; CD8+ T cell isolation kit, Miltenyi) according to the manufacturer’s instructions. Purity was assessed by flow cytometry on a BD LSRFortessa Flow Cytometer using anti-mouse CD4 (RM4-5, 1:400) and anti-mouse CD8 (Ly-3, 1:400) antibodies. Cells were plated on 48-well plates, coated with anti-CD3 (1 μg ml1) and anti-CD28 (10 μg ml1) antibodies, in RPMI medium supplemented with 10% FCS, penicillin, streptomycin, HEPES, glutamine, pyruvate, nonessential amino acids and β-mercaptoethanol diluted with PBS (1:1) in the presence of IL-12 (3 ng ml1, Peprotech) (TH1 conditions). Cultures were supplemented on days 0, 1 and 2 with 5 mM NaCl or 5 mM BHB. Mouse CD4+ T cells were collected at days 3 and 6 of culture. Viability was assessed by Zombie UV Fixable Viability Dye (BioLegend) and cytokine production was measured by intracellular cytokine staining after 3 h stimulation with PMA (50 ng ml1) (BioGems) and ionomycin (1 µg ml1) (BioGems) in the presence of brefeldin A (1 μg ml1) (GolgiPlug, BD Biosciences). Cells were stained for viability and surface markers, fixed with 3.7% formaldehyde (Sigma), permeabilized with 0.1% NP-40 and stained for intracellular cytokines.
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5

Flow Cytometry Analysis of SVF

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The SVF of WAT was incubated with Fc blocker (Biolegend) and then stained with fluorochrome-conjugated antibodies against CD11b (M1/70), CD45 (30-F11), ST2 (DIH9), CD206 (C068C2), CD11c (N418) (Biolegend), and F4/80 (T45-2342) (BD Biosciences, San Jose, CA) or corresponding isotypic antibodies in dark at 4 °C for 30 min. Dead cells were excluded by staining with Zombie UV Fixable Viability dye (Biolegend). Data were acquired on Aria III (BD Biosciences) or CytoFLEX (Beckman Coulter, Brea, CA) and analyzed with FlowJo software (Tree Star) or CytExpert (Beckman Coulter).
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6

Flow Cytometric Immunophenotyping of Leukocytes

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Leukocyte viability was determined by staining with Zombie UV Fixable Viability Dye (BioLegend, San Diego, CA). Cells were incubated for 5 min at 4 °C with anti-CD16/32 (Becton Dickinson; BD, San Jose, CA, 2.4G2), then stained with the following antimouse antibodies: CD45.1 (Thermo Fisher, A20), CD45.2 (Thermo Fisher, 104), CD11b (Thermo Fisher, M1/70), CD11c (BD, HL3), Ly6C (BioLegend, HK1.4), Ly6G (BD, 1A8), F4/80 (BD, T45-2342), B220 (Thermo Fisher, RA3-6B2), NKp46 (BD, 29A1.4), CD3 (Thermo Fisher, 17A2), MHCII (Thermo Fisher, M5/115.15.2), and Siglec-F (BD, E50-2440). Cells were fixed with stabilizing fixative (BD), and data were acquired on a BD Special Order Research Product LSRFortessa flow cytometer. Quality control checks with Cytometer Setup and Tracking beads (BD) and Ultra Rainbow Calibration Particles (Spherotech, Lake Forest, IL) were performed before each acquisition. Data were cleaned using FlowAI32 (link) and analyzed using Flowjo software (BD).
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7

Bone Marrow Cell Isolation and Analysis

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Bone marrow single-cell suspensions were made by flushing femurs and tibiae with PBS + 2% fetal calf serum (FCS). All cell suspensions were treated with ACK buffer for red cell lysis. For flow cytometic analysis cell suspensions were stained with the appropriate combination of the following antibodies: anti-FceRI-PE (MAR-1; BioLegend); ant-CD49b-PE-Cy7 (DX5; Biolegend); anti-CD90.2-APC (30-H12; Biolegend); anti-CD19-APC (1D3; eBioscience); anti-IgM-PE-Cy7 (RMM-1; Biolegend); anti-IgD-eFluor450 (11-26; eBioscience); anti-CD93-PE (AA4.1; Biolegend); anti-CD2-FITC (RM2-5; BD Biosciences). Dead cells were excluded with Zombie UV Fixable viability dye (BioLegend). For cell cycle analysis and Nicoletti assay cells were fixed with the FOXP3/Transcription Factor Staining Buffer Set (eBioscience) and DNA was stained with 4,6 diamidino-2-phenylindole (DAPI; BioLegend). Flow cytometry was conducted using an LSRFortessa 5-laser (325; 405; 488; 561; 632) configuration (BD Biosciences). For FACS cells were collected using a MoFlo Astrios (Beckman Coulter) and sorted directly into Opti-MEM+ 10% FCS Media.
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8

Multicolor Flow Cytometry of THP-1 and Blood

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Flow cytometry analysis of THP-1 cells and total blood was performed using the following antibodies. Conjugated anti-human SR-B1 APC (Miltenyi Biotec 130-111-237), CD235a APC Cy7 (BioLegend 3,49,115), CD45 BUV805 (BD Biosciences 6,12,892), CD56 BUV 737 (BD Biosciences 6,12,767), CD11c PeCy7 (BioLegend 3,37,216), CD11b PE (eBioscience 12-0118-41), CD3 PerCP Cy5.5 (BD Biosciences 5,60,835), CD19 BV786 (BioLegend 3,02,239), HLA-DR BUV 395 (BD Biosciences 7,40,302), CD14 BV605 (BioLegend 3,01,834). Labeling of mouse blood was done using the following conjugated antibodies: CD45.2 PE (eBioscience 12-0454–82), CD115 PerCPeF710 (eBioscience 46-1,152-82), CD11b BV650 (eBioscience 48-0112–20), Ly6G BV510 (BD Biosciences 5,63,402), CD3 APC-eF780 (BioLegend 47-0032–82). Fc receptors were blocked using FCR blocking reagent (Myltenyi Biotec). Surface membrane staining was performed in PBS FBS 2%. The Zombie UV fixable viability dye (BioLegend 4,23,107) was used to exclude dead cells. Samples were acquired on a Cytoflex (Beckman Coulter) and analyzed with FlowJo 10 (BD Biosciences).
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9

Comprehensive Immune Cell Profiling

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Single cell suspensions were prepared from spleen, mesenteric lymph nodes (MLN), inguinal lymph nodes (ILN), PP, and thymus using 70μm nylon cell strainers. Intrahepatic lymphocytes were isolated using steel mesh (150 μm). Cells were resuspended in 40% isotonic Percoll (GE Healthcare) and centrifuged at 930g at room temperature for 20 min. Red blood cells were lyzed with ACK solution before antibody staining. The cells were preincubated for 20 min with anti-CD16/32 Fc blocking antibody (2.4G2) and with Zombie UV™ Fixable Viability Dye (Biolegend). Cell surface staining for flow cytometry was done using a combination of the following antibodies: anti-CD45.2 (104), anti-CD3 (17A2), anti-B220 (RA3-6B2), anti-CD4 (GK1.5), anti-CD8 (53-6.7), anti-NK1.1 (PK136), anti-TCRβ (H57-597), anti-GL-7 (GL7), anti-IgG (A85-1), anti-IgA (mA-6E1), anti-IgM (RMM-1), anti-CD138 (281-2), anti-CD19 (ID3), anti-CD11b (M1/70), anti-Ly6G (IA8). iNKT cells were identified using FITC conjugated mCD1d−αGalCer tetramers (PBS57, NIH tetramer Core). All antibodies were purchased from BD Biosciences, Biolegend or eBioscience. Flow cytometry analysis was performed on a BD FACSCelesta and analyzed using FlowJo 10 software.
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10

Isolation and Characterization of Prostate Stem Cells

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This process was a modification of a well-established protocol12 (link), 39 (link). Briefly, minced prostate tissues were digested in 1 mg/mL collagenase (Sigma-Aldrich) in RPMI-1640 (Gibco) media containing 10% FBS (Corning) with shaking at 37°C for 2 hours, followed by trypsinization. Dissociated cells were passed through 20G needles and 40 μm cell strainers to eliminate aggregates, followed by removal of red blood cells by ACK buffer. To enrich murine bPSC, isolated cells were stained with Zombie Violet Live/Dead Fixable Viability Dye (Biolegend) in PBS, followed by incubation with 1:100 diluted fluorescence-conjugated specific antibodies (Biolegend): CD45-FITC (#103108), CD31-FITC (#102506), Sca-1-APC (#122512) and CD49f-PE (#313612). Human prostate samples from unidentified patients were acquired from Indiana University School of Medicine Tissue Repository under IRB-approved protocols. Isolated human prostate cells were stained with Zombie UV Fixable Viability Dye (Biolegend), CD45-FITC (#304006), EpCAM-PE (#324206), CD26-APC (#302710) and CD49f-BV421 (#313624) as described in detail by Strand et al.40 (link). Once stained, fluorescence activated cell sorting was performed on the BD FACSAria under sterile conditions.
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