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172 protocols using live dead fixable violet dead cell stain kit

1

Flow Cytometry Analysis of Syndecan Expression and Cell Proliferation

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Flow cytometry was used to detect cell surface syndecan (SDC) expression and cell proliferation by staining for Ki-67. To evaluate SDC expression, VK2/E6E7 cells were exposed to MPA and then stained (separately) with anti-human syndecan-2-allophycocyanin and anti-human syndecan-3-allophycocyanin (R&D Systems), and then fixed in 4% paraformaldehyde (BD Biosciences). To evaluate cell proliferation, VK2/E6E7 were treated with MPA, stained with LIVE/Dead fixable violet dead cell stain kit (Life Technologies), fixed and permeabilized with Cytofix/Cytoperm Fixation/Permeabilization Solution Kit (BD Biosciences), and finally stained with Alexa Fluor 700 mouse anti-human Ki-67 antibody (BD Pharmigen). To evaluate proliferation of MPA-treated T cells, PBMC were stained with anti-human CD3-phycoethrithrin (PE) (BD Pharmigen), anti-human CD4-FITC (BD Pharmigen), anti-human CD8-APC (BD Pharmigen), and LIVE/Dead fixable violet dead cell stain kit (Life Technologies), cells were then permeabilized and stained with Alexa Fluor 700 mouse anti-human Ki-67 antibody as previously described. Flow cytometric analysis was performed using a BD LSRII (BD Bioscience). FCS files were analyzed using FlowJo version 9.4.9 (TreeStar). Ten thousand live events were acquired per sample; fluorescence minus one negative control for SDC2, SDC3, and Ki-67 were used for gating.
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2

TNF-α Stimulation of Endothelial Cells

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For TNF-α stimulation, confluent monolayers of primary endothelial cells were stimulated with 10 ng/ml TNF-α for 20 h at 37°C. For flow cytometry, cells were rinsed with Hanks balanced salt solution and lifted with 10 mM EDTA. EPCR was detected by a goat anti-human EPCR polyclonal antibody (30 µg/ml; R&D), followed by a fluorescently labeled secondary antibody. ICAM-1 was detected by a phycoerythrin-labeled mouse MAb (0.5 µg/ml; Abcam ab19756). CD36 was detected by a fluorescein isothiocyanate (FITC)-conjugated mouse MAb (clone TR9, 10 µl/105 cells; Abcam ab39022), and CD31 was detected by an FITC-conjugated mouse MAb (clone B-B38, 1 µl/105 cells; Abcam ab27333). Prior to LSRII analysis, cells were fixed with 2% (wt/vol) paraformaldehyde for 10 min. Single live cells were gated with the Live/Dead fixable violet Dead cell stain kit (Molecular Probes), and data were analyzed with FlowJo v10 software.
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3

FAP Antigen Characterization in Mice

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Biotinylated anti-FAP (Clone 73-3) antibody was generated in-house, and detected using Streptavidin-APC (BioLegend). The specificity of the anti-FAP antibody was verified based on reactivity with cells from wild-type but not FAP-null mice. Dead cells were excluded by using the Live/Dead Fixable Violet Dead Cell Stain Kit (Molecular Probes). Staining with anti-αSMA antibody (Sigma, clone1A4, FITC) was performed after permeabilizing cell suspensions with the Cytofix/Cytoperm Fixation/Permeabilization Kit (BD Biosciences), as per the manufacturer’s instructions.
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4

Multiparameter Flow Cytometry of CD30, CD46, and CD150

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Expression of human CD30 was detected by a phycoerythrin (PE)-labeled mouse CD30 antibody (clone: Ki-2, Miltenyi Biotech, Germany). Human CD46 was detected by a fluorescein isothiocyanate (FITC)-labeled mouse CD46 antibody (clone: MEM-258, BioLegend, USA). Human CD150 (SLAM) was detected by a PE-labeled mouse CD150 (SLAM) antibody (clone: A12 (7D4), BioLegend, USA). Viability of cells was analyzed using the LIVE/DEAD Fixable Violet Dead Cell Stain Kit (Molecular Probes, USA). Flow cytometry analysis was performed using the MACSQuant Analyzer 10 (Miltenyi Biotec, Germany) and data were analyzed using FCS Express version 4.
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5

Isolation and Analysis of Naive CD4+ T Cells

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CD4+CD62L+ T Cell Isolation Kit II, mouse (Miltenyi Biotec, 130-093-227); Naive CD4+ T Cell Isolation Kit, mouse (Miltenyi Biotec, 130-104-453); FITC BrdU Flow Kit (BD Pharmingen, 51-2354AK); LIVE/DEAD™ Fixable Violet Dead Cell Stain Kit (Molecular probes, L34955); CellTrace™ Violet Cell Proliferation Kit (Molecular probes, C34571); Mouse IL-13 ELISA Ready-SET-Go Kit (eBioscience, 88-7137-22); Mouse IL-4 ELISA Ready-SET-Go Kit (eBioscience, 88-7044-88); Mouse IL-5 ELISA (BD Biosciences, 555236); PE Mouse anti-XBP1S Clone Q3-695 (BD Pharmingen, 562642); XBP1 (M-186)X- (Santa cruz, Sc 7160x); IL5-PE (BD Pharmingen, 554395); IL4-APC, Clone 11B11 (eBioscience, 17-7041-82); IL13-AF488, Clone eBio3A (eBioscience, 53-7133-82); IFNγ-Per CP Cy5.5, Clone XMG1.2 (eBioscience, 45-7311-82); FACS Staining buffer (eBioscience, 00-4222-26); IC Fixation buffer (eBioscience, 00-8222-49); Fixation/Permeabilization Diluent (eBioscience, 00-5223-56); Fixation/Permeabilization concentrate (eBioscience, 00-5123-43); Permeabilization buffer (eBioscience, 00-8333-56); SV Total RNA Isolation System (Promega, Z3101); Transcriptor High Fidelity cDNA Synthesis kit (Roche, 05081955001); SYBR™ Select Master Mix (Applied Biosystems, 4472908); Western blot antibodies: IRE1α (14C10) Rabbit mAb (Cell Signaling, #3294), IRE1 alpha [p Ser724] Antibody (Novus biologicals,NB100-2323).
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6

Chlamydia-specific T cell response

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Chlamydial-specific T cell expansion and cytokine production from PBMC was done as described (14 (link)). Briefly, CFSE (carboxy fluorescein succimidyl ester, Molecular Probes) labeled PBMCs were incubated at 2 x106 cell/ml in deep well tissue culture plates (96 well, Eppendorf) in 1 ml of AIM V medium (Life Technologies) only or pulsed with C. trachomatis A2497P+ elementary bodies (EB) (MOI= 20) or chlamydial soluble antigen (SA) (100 μg/ml) and incubated for five days at 37°C and 5% CO2. Cells were then re-stimulated for six additional hours with medium only or chlamydial antigens in the presence of mAb co-stimulatory signals. The mAb used were 0.5 μg/ml of anti-CD28 (clone CD28.2, Nonhuman Primate Reagent Resource, University of Massachusetts Medical School, Boston, MA), Mab CD49d (clone 9F10, BD Biosciences) and 1X brefeldin A solution (BD Biosciences). The cells were washed and analyzed by flow cytometry. A Live/Dead fixable violet dead cell stain kit (Molecular Probes) was used to discriminate live and dead cells. Dilution of CFSE stain was used to monitor proliferation of CD3+CD4+ and CD3+CD8+ T cells. The percent of cells proliferating was normalized against their respective negative controls which were cells incubated with sucrose-phosphate glutamate buffer (SPG) or SA prepared from mock-infected BGMK monolayers.
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7

Evaluating Cytokine-Producing Lymphocytes

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To evaluate the ratio of cytokine-producing lymphocytes, spleen cells were cultivated in the absence or presence of nanostructures VarA4, VarB, VarC and VP1 control (VP1Con) (50 μg/ml), and PMA (20 ng/ml Sigma), ionomycin (500 ng/ml, Sigma) and brefeldin A (5 μg/ml, eBioscience) were added to the cultures for the last 5 h of the 48-h incubation period. The cells were harvested and washed with PBS containing 0.5% BSA. Before intracellular staining, the cells were incubated for 30 min on ice with Alexa Fluor 700-labelled anti-CD45 antibody (clone 30-F11, BioLegend) and a Live/Dead Fixable Violet Dead Cell Stain Kit (Molecular probes, Eugene, OR) to stain dead cells. For intracellular staining, the cells were fixed and permeabilized using a Fixation/permeabilization Buffer Staining Kit (eBioscience) according to the manufacturer’s instructions. For detection of cytokine-producing lymphocytes, the cells were stained with the following mAbs: FITC-labelled anti-IFNγ antibody (clone, XMG1.2, BioLegend) and PE-labelled anti IL-4 antibody (clone 11B11, eBiosciences) for 30 min at 25°C. Data were collected using a LSRII flow cytometer (BD Biosciences) and analyzed using Gatelogic 400.2A software.
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8

Lipid Nanoparticle Preparation and Characterization

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Sucrose, glucose, HEPES (4–2(2-hydroxymethyl)-1-piparazineethane-sulfonic acid), sodium chloride, and hydrochloric acid (HCl) were purchased from Fisher Scientific. Ammonium sulfate, sodium phosphate, potassium phosphate, potassium chloride, sodium bicarbonate, lectin protein from Canavalia ensiformis, ATTO-488 NHS-ester, TCEP (tris(2-carboxyethyl) phosphine hydrochloride), and doxorubicin were purchased from Sigma-Aldrich. Fetal bovine serum (FBS), trypsin, penicillin, streptomycin, L-glutamine, PBS (phosphate buffered saline), and DMEM (Dulbecco’s modified Eagle medium) were purchased from GE Healthcare. Texas Red-DHPE (Texas Red-1,2-Dihexadecanoyl-sn-glycero-3-phosphoethanolamine) was purchased from Thermofisher. Trypan blue was purchased from Life Technologies. DPPC (1,2 – dipalmitoyl-sn-glycero-3-phosphocholine), DOPC (1,2 dioleoyl-sn-glycero-3-phosphocholine), cholesterol (from ovine wool), DOTAP (1,2 dioleoyl--3-trimethylammonium-propane), and PEG2000-DPPE (1,2 dipalmitoyl-sn-glycerol-3-phosphoethanolamine-N-[Methoxy(Polyethylene glycol)-2000]) were all purchased from Avanti Polar Lipids (Alabaster, AL). LIVE/DEAD fixable violet dead cell stain kit was purchased from Thermo Fisher Scientific. All reagents were used without further purification.
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9

Monitoring T Cell Activation via Flow Cytometry

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Every 24 h from 0 h to 72 h post T cell activation, cells were stained with the LIVE/DEAD Fixable Violet Dead Cell Stain Kit (Thermo scientific, https://www.thermofisher.com) and CD8a-PE (Biolegend, San Diego, USA, 100709) in 2% FBS/PBS on ice for 30 min. Cells were collected on a Fortessa flow cytometer (BD Bioscience, Haryana, India) and analyzed using FlowJo software (Version 10.1). The mean forward scatter (FSC-A) of CD8+, live cells was gated as a measure of cell size during T cell activation.
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10

Murine Pancreatic Cell Isolation

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Murine pancreata were resected, and tissue was dissociated using the mouse tumor dissociation kit (Miltenyi, Bergisch Gladbach, Germany) per the manufacturer’s protocol. Dissociated tissue was sequentially passed through 500 μm (Repligen, Boston, MA), 105 μm (Repligen), and 40 μm (Thermo Fisher Scientific) filters to acquire a single-cell suspension before magnetic isolation of CD45+ cells. Cells were incubated with CD45+ MicroBeads (Miltenyi) followed by magnetic separation using LS Columns (Miltenyi) on a QuadroMACS magnet (Miltenyi) per the manufacturer’s protocol. CD45+ cells were then labeled with LIVE/DEAD Fixable Violet Dead Cell Stain Kit (Thermo Fisher Scientific) before subsequent fixation and staining using the PerFix-nc kit (Beckman Coulter, Brea, CA) as per the manufacturer’s protocol. Antibodies are described in detail in Key Resources Table. The Attune NxT (Thermo Fisher Scientific) was used for multicolor flow cytometric detection, and analysis was done using FlowJo (BD Biosciences).
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