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158 protocols using facsdiva v8

1

CD24 and CD44 Expression Analysis

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For the analysis of CD24 and CD44 expression on cell membrane, 5 × 105 of cells were collected in Cell Staining Buffer (BioLegend, #420201) and stained with PE-Cy™7-conjugated anti-CD24 (1:100 for 20 min; BD Biosciences, #561646) and APC-conjugated anti-CD44 antibody (1:60 for 20 min; BD Biosciences, #559942) by using PE-Cy™7 Mouse IgG2a (1:100 for 20 min; BD Biosciences, #552868) and APC Mouse IgG2b (1:60 for 20 min; BD Biosciences, #555745) as control staining. Stained cells were analyzed by BD FACSCanto II cytometer and data were acquired by BD FACSDiva v8.0.2 software and processed by FlowJo v10.7.1 software (BD Biosciences). ALDEFLUOR assay was carried out using the ALDEFLUOR assay kit (STEMCELL Inc., #101700) according to the manufacturer’s instructions. The ALDH1 inhibitor, diethylaminobenzaldehyde (DEAB), was used as a negative control. The processed cells were evaluated by BD FACSCanto II cytometer and data were acquired by BD FACSDiva v8.0.2 software and analyzed by FlowJo v10.7.1 software (BD Biosciences).
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2

Quantifying BCMA-specific CTL Proliferation

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Proliferation of CFSE (Molecular Probes) labeled BCMA-specific CTL (CD8+ gated) was measured after co-culture with irradiated myeloma cells. On days 3-6 of co-culture, the cells were stained with specific mAbs, and acquired by flow cytometry. To measure anti-tumor activities, BCMA-CTL were mixed with the respective target in the presence of CD107a mAb. After 1 hour of co-culture, Brefeldin A and Monensin (BD) were added and cultures were incubated for an additional 5 hours at 37°C. Cells were harvested, stained with Live/Dead-Aqua and fluorochrome conjugated mAbs, fixed/permeabilized, and stained intracellularly with specific mAb against IFN-γ, IL-2 or TNF-α, acquired using a LSRII Fortessa™ flow cytometer (BD) and analyzed using FACS DIVA™ v8.0 (BD) or FlowJo v10.0.7 (Tree star, Ashland, OR) software
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3

Peptide Uptake by Dendritic Cells

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Monocyte-derived dendritic cells (DC) were generated as described previously.7 (link)-9 (link) Immature DC (1 x 106 cells/well) were pulsed with free BCMA peptide-FITC or the peptide-FITC encapsulated nanoparticles in the presence of human β2-microglobulin (3 μg/ml) and incubated at 37°C. Cells were washed, fixed in 2% paraformaldehyde, acquired using a LSRII Fortessa™ flow cytometer (Becton Dickinson (BD), San Jose, CA). The level of peptide loading was analyzed in a time-dependent manner using FACS DIVA™ v8.0 (BD) or FlowJo v10.0.7 (Tree star, Ashland, OR) software. The peptide uptake was also imaged by confocal microscopy (Nikon, Tokyo, Japan), upon fixation of the cells with 2% paraformaldehyde (Electron Microscopy Sciences, Hatfield, PA) and counter-stained with 300 nM DAPI (Sigma-Aldrich) to identify cell nuclei.
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4

Multicolor Flow Cytometry of B Cell Subsets

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Nonspecific binding was blocked with an anti-FcγIII/II antibody (anti-CD16/32; BD Pharmingen, Heidelberg, Germany). The following antibodies and conjugates were used in the experiments in appropriate combinations: anti-CD5-phycoerytrhin (PE)/Cy7 (clone 53-7.3) (Biolegend, San Diego, CA, USA), anti-CD19-eFluor 660 (clone 1D3) (eBioscience, Thermo Fisher Scientific, Waltham, MA, USA), anti-CD23-PE (clone B3B4) (eBioscience), anti-CD3-FITC (clone 145-2c11), anti-CD11b-APC-eFluor 780 (clone M1/70) (eBioscience), anti-IgD-V450 (clone 11-26c.2a) (BD Biosciences), and anti-IgM-BV650 (clone R6-60.2) (BD Biosciences). For dead cell exclusion, cells were stained with 7-AAD Viability Staining Solution (Biolegend) before analysis. Stained cells were analysed on a BD LSR II Flow Cytometer (BD Biosciences) and evaluated with FlowJo software (Version 10, LLC, Ashland, OR, USA). The applied gating strategy is shown in Supplemental Figure S2. Fluorescence-activated cell sorting was performed on a FACSAria III cell sorter and gated in FACSDiva v8.0 (BD Biosciences). B1a B cells were identified as CD19+CD5+CD23IgM+IgD, B1b B cells as CD19+CD5CD23IgM+IgD, and B2 B cells as CD19+CD5CD23+IgMlowIgD+.
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5

Apoptosis Analysis of Cell Lines

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A549 and SK-MES-1 cells transfected with the CNN3-ov or NC recombinant plasmids for 48 h were collected and washed twice with ice-cold PBS. Subsequently, the cells were resuspended and stained according to the instructions of the Annexin V-FITC/PI Apoptosis Detection kit (Nanjing KeyGen Biotech Co., Ltd.). The percentage of apoptotic cells was assessed using a BD FACSCanto flow cytometer (BD Biosciences) and cells were analyzed using FACSDiva v8.0 (BD Biosciences). This experiment was performed in triplicate.
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6

Comprehensive Immune Cell Profiling

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Cells, isolated from peripheral lymph nodes, mesenteric lymph nodes, spleen and lamina propria were stained with Sytox blue or Live/dead fixable viability dye (Life technologies and eBioscience respectively) together with the appropriate conjugated αCD3, αCD45.2, αCD62L, αCD4, αCD8, αCD44, αTCRγδ, αCD19, αNK1.1, αGrl, αCD11b, αCD11c, and αFoxp3 (eBioscience or Becton Dickinson, San Diego, CA).
IL6, IL12, TNFβ, IL-10, MCP-1 and IFNγ production was assessed in the culture supernatant of LPS/IL4-activated splenocytes using a Cytometric Bead Array (CBA) Kit (BD Biosciences). To assess intracellular cytokine production, freshly isolated and anti-CD3/CD28 stimulated LN cells were activated with PMA (Sigma-Aldrich; 100 ng/ml)/Ionomycin (Sigma-Aldrich; 1 μg/ml) in the presence of brefeldin A (Sigma-Aldrich; 10ug/ml) for 4h at 37°C, fixed, permeabilized and then stained with specific antibodies against IL2 and IFNγ.
Foxp3 staining was performed following fixation/permeabilization (eBioscience). Stained cells were assessed by flow cytometry (LSR Fortessa, Becton Dickinson, San Jose, CA) and data were analyzed by FACSDiva (v.8.0, BD Biosciences) and FCAP Array Software (CBA analysis).
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7

Comprehensive T Cell Immunophenotyping

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Frozen cells were thawed, washed and cultured in cRPMI (106/mL) with or without 0.5x cell stimulation cocktail (eBiosciences) and stained with viability dye (Invitrogen) and anti-CD3, -CD4, -CD8, -CD45RA, -CCR7, -CD95 (BD), -CXCR5 and -PD-1 (eBiosciences) antibodies. Intracellular staining was performed with anti-FoxP3, -IFN-γ (BD), -IL-21, -IL-4 (eBiosciences) antibodies after permeabilizing fixed cells with the Human FoxP3 Buffer Set (BD) per the manufacturer’s recommendations. T follicular cells (TFH) were defined as live CD3+CD4+CD95+CCR7loCXCR5+PD-1hi cells; T follicular regulatory cells (TFR) were FoxP3+ TFH. T helper cells (TH) were live CD3+CD4+CD95+CXCR5-PD-1lo; T regulatory cells (TREG) were FoxP3+ TH25 (link), 26 (link). A total of 300,000 events were collected using an LSRII or LSRFortessa using FACSDiva v8.0 (BD) and analyzed with FlowJo Software v10.2 (TreeStar) applying fluorescence-minus-one controls and Boolean gating.
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8

Flow Cytometry for Immune Profiling

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For surface antigen identification, cellular pellets obtained after CSF centrifugation were resuspended in the residual volume (about 100 µl), stained with the appropriate amounts of monoclonal antibodies for 30 minutes at 4°C in the dark, washed twice with PBS, and analyzed in a FACSCanto II flow cytometer (BD Biosciences). For intracellular cytokine detection, cellular pellets were stimulated and stained for flow cytometry analysis as described previously (20 (link)). In brief, cellular pellets were incubated for 4 hours at 37°C in 5% CO2 with 50 ng/ml Phorbol 12-myristate 13-acetate (PMA) (Sigma-Aldrich, St. Louis, MO) and 750 ng/ml Ionomycin (Sigma-Aldrich) in presence of 2 µg/ml Brefeldin A (GolgiPlug, BD Biosciences) and 2.1 µM Monensin (Golgi Stop, BD Biosciences). After incubation, cells were washed and stained with the monoclonal antibodies recognizing the surface antigens. Then, cells were washed, fixed and permeabilized with Cytofix/Cytoperm Kit (BD Biosciences), washed twice and subjected to intracellular staining with monoclonal antibodies recognizing different cytokines. Then, cells were washed and analyzed in a FACSCanto II flow cytometer. Data analysis was performed using the software FACSDiva V.8.0 (BD Biosciences) and the gating strategy shown in Supplementary Figures 2, 3. All labeled cells were acquired to calculate total cell numbers.
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9

Comprehensive B-cell Immunophenotyping

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One million thawed PBMC were incubated with 11‐color antibody cocktails against B‐cell markers for 15 minutes at room temperature in 100 µL total volume (Table S3). Flow cytometric analyses were performed on a 4‐laser LSRFortessa (BD Biosciences), and data were analyzed using FACSDiva V8.0 (BD Biosciences). B‐cell subsets were defined as described previously.41, 45, 46 Briefly, within the CD19+ B‐cell population, the proportions were determined of plasmablasts (CD27+CD38high), transitional (CD27CD38high), naive mature (CD27IgM+IgD+), natural effector memory B cells (CD27+IgM+IgD+), and IgM‐only memory B cells (CD27+IgM+IgD). Furthermore, we analyzed Ig switched CD27CD38dim and CD27+CD38dim memory B cells expressing IgA, IgE, IgG, or each of the 4 IgG subclasses.
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10

Cell Cycle Analysis by Flow Cytometry

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Treated cells were collected in a flow tube, washed with 3–4 ml PBS and centrifuged (300 × g for 10 min at 4°C). Upon discarding the supernatant, ≥5 ml pre-cooled 70–80% ethanol was slowly added, and the cells were then vortexed and mixed overnight at 4°C. Next, the cells were centrifuged at 300 × g for 10 min at 4°C and the supernatant was discarded. The cells were then washed twice to remove all ethanol. Next, the cells were stained by resuspending in 0.5 ml FxCycle™ PI/RNase Staining Solution (cat. no. F10797; Thermo Fisher Scientific, Inc.), and incubating for 15 min at room temperature in the dark. Next, the cells were analyzed using a flow cytometer (FACSDiva™; V8.0; BD Biosciences) within 1 h (22 (link)). ModFit software (ModFit LT; version 3.3; BD Biosciences) was used for processing and analyzing the results.
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