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21 protocols using fixation and permeabilization solution kit

1

Antigen-specific T cell phenotyping

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Cells were stained for flow cytometry in FACS buffer (PBS, 1% BSA, and 1 mM EDTA) and antibodies at 4°C for 30 minutes, and then fixed in 1% paraformaldehyde for 30 minutes. Antigen-specific CD8 T cells were gated by CD8+CD44+CD62L-Tetramer+ (including gp33, gp276 and np396 tetramers). Activated CD4 T cells were gated on CD4+CD44+CD62L− markers. Antibodies used included CD4 PerCP-Cy5.5 (clone RM4.5, Tonbo Biosciences, San Diego, CA), CD8 FITC (clone 53–6.7, Tonbo Biosciences), CD44 APC-Cy7 (clone IM7, BioLegend, San Diego, CA), CD62L Alexa Fluor 700 (clone MEL-14, BioLegend, San Diego, CA), CD69 PE-Cy7 (Clone H1.2F3, BioLegend, San Diego, CA) CD127 BV510 (Clone SB/199, BD Horizon), PD-1 PE (clone RMP1–30, BioLegend, San Diego, CA). gp33 var C41M (KAVYNFATM), gp276 (SGVENPGGYCL), and np396 (FQPQNGQFI) biotinylated monomers on H-2Db were obtained from the NIH Tetramer Core facility at Emory University and tetramerized to streptavidin-APC (Prozyme). Flow cytometry was performed on a BD LSR II and analyzed using FlowJo 9.6.4 software. Intracellular cytokine staining was performed using the Fixation and Permeabilization Solution Kit with BD GolgiPlug (Becton, Dickinson and company) according to the manufacturer’s protocols.
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2

Immunophenotyping of Monocyte-derived DCs

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PE-conjugated anti-human CD11c (Becton Dickinson) was used for monocyte-derived DCs (MoDCs) and iPSDCs staining. Intracellular staining with an anti-human MSLN monoclonal antibody (EPR19025-42, Abcam) and Alexa Fluor 488 conjugated goat anti-rabbit IgG antibody (Abcam) was performed using a Fixation and Permeabilization Solution Kit (Becton Dickinson).
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3

Canine T-cell Phenotyping and IFNγ Detection

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The following monoclonal antibodies were used in these studies: mouse anti-canine CD3-FITC (clone CA17.2112), CD4-RPE or APC (clone YKIX302.9), CD8 RPE or APC (YCATE55.9), and mouse-anti-bovine IFNγ-RPE (clone CC302) all from AbD Serotec (Raleigh, NC). The bovine IFNγ-specific clone CC302 has been previously demonstrated to cross-react with canine IFNγ [28 (link)].
For surface staining, cells were resuspended at 107 cells/mL in FACS buffer (0.1% NaN3, 10% fetal calf serum, PBS) and incubated for 20 minutes at 4°C with 10 μg/mL primary antibodies or as recommended by the manufacturer. Cells were washed and fixed in BD FACS Lysis buffer (BD Biosciences).
Intracellular cytokine staining for IFNγ was carried out using the BD Fixation and Permeabilization Solution kit (BD Biosciences). Cells were cultured with antigen for 5 days, and then Brefeldin A was added for the last 5–6 hours of incubation. Cells were surface stained and then fixed, permeabilized and stained for intracellular IFNγ (Clone CC302, 10 μg/mL) per manufacturer’s instructions.
Flow cytometry data were collected on a BD LSR Fortessa X-20 flow cytometer and analyzed using FlowJo software (Tree Star Inc., San Carlos, CA).
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4

Flow Cytometric Analysis of Alveolar Macrophages

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Cells isolated from BALF samples were first incubated with Fc block (eBioscience) and, then, cell surface staining was carried out by incubation with APC-conjugated anti-mouse CD11c and FITC-conjugated anti-mouse Siglec F. Following fixation and permeabilization (BD Fixation and Permeabilization Solution Kit, BD Biosciences), intracellular staining was performed by incubation with PE-conjugated anti-mouse Arg-1 and PE-CY7-conjugated anti-mouse iNOS. The proper isotype controls were used in each case. Flow cytometry events were gated first based on forward and side scatter. Then, CD11c+ Siglec F+ cells (21 (link),22 (link)) (for in vivo AMs) were selected to evaluate the expression of Arg-1 and iNOS, respectively. Each flow cytometry analysis experiment was run on at least 100,000 cells and data were acquired using a BD FACSCantoTM II instrument and analyzed using the FlowJo X software.
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5

Multiparameter Immune Cell Profiling

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For cell surface staining, cells were collected and washed and stained in FACS buffer (PBS, 1% BSA, 1mM EDTA, 0.01 NaN3). Human DC-SIGN/CD209 PE-conjugated Antibody (R&D, #FAB161P-025) and anti-human CD45 AF700 (Biolegend, #304024) are for MDDC surface staining. For intracellular cytokine staining, cells were incubated with GolgiPlug 30min before adding TLR agonists. After 5 hours TLR ligands stimulation, the cells were fixed and permeabilized using BD Fixation and Permeabilization Solution Kit with BD GolgiPlug (Cat. No. 555028) and stained with APC anti-human TNF-α Antibody (BioLegend, #502913).
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6

Quantifying Pancreatic Islet Viability

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Human pancreatic islets of non-diabetic subjects were cultured with standard medium, or in the presence/absence of IGFBP3 and/or in the presence/absence of Ecto-TMEM219 for 72 h as previously described (see “Pancreatic islets and Interventional studies”). Islets were detached with Versene (ThermoFisher Scientific) and stained with the BD Horizon™ Fixable Viability Stain 510 (FVS510, BD Biosciences 564406, San Jose, CA), which ensures accurate assessment of cell viability in samples after fixation and/or permeabilization as per manufacturer’s instructions. After being stained with BD Horizon™ Fixable Viability Stain 510, cells were next fixed and permeabilized with Fixation and Permeabilization Solution Kit (554714, BD Biosciences, San Jose, CA)51 (link) and finally stained with guinea pig anti-insulin antibody (1:200, Guinea Pig, ThermoFisher Scientific, PA1-26938) followed by AlexaFluor488 anti-guinea pig (1:200, ThermoFisher Scientific, A-11073). Flow cytometry analysis was performed using a BD FACS Celesta flow cytometry system (BD Biosciences) and analyzed using Flowjo software (Version 6 and Version 10, Tree Star, Ashland, OR).
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7

Immune Cell Profiling by Flow Cytometry

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The antibodies we used in this study were anti-mouse CD4, CD19, CD45, B220, CD3, F4/80, CD11c, CD11b (BD Bioscience), IL-10, IL-17, IFNγ, IL-27p28 and Foxp3 (eBioscience), eBi3 (R&D systems) and LIVE/DEAD Cell Viability Kits (Invitrogen). MLN or colonic LP cells were collected and incubated for 15 minutes at 4°C with anti-CD16/CD32 (BD Bioscience) and then for 20 minutes at 4°C with antibodies for cell surface and LIVE/DEAD Cell Viability Kits to evaluate the cell phenotype and CD4+ T cell/B cell reconstitution. Enumeration of cells expressing IL-10, IL-17, IFNγ, IL-27p28, Ebi3 and Foxp3 was performed by intracellular staining with a Fixation and Permeabilization Solution Kit (BD Bioscience) according to the manufacturer's instructions. For intracellular cytokine staining, 100ng/ml PMA, 1µg/ml Ionomycin (Sigma-Aldrich) and Golgi stop (BD Biosciences) were added into the medium during the last 4 hours of the culture period. Cells were washed and then analyzed on a CyAn flow cytometer (Beckman Coulter, Brea, CA, USA). Proper isotype antibodies were used as a control and gated live CD45+ cells were analyzed with Summit 5.2 software (Beckman Coulter)
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8

HIV Activation Monitoring in Microglial Cells

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Flow cytometry analysis was performed to detect the expression of GFP as a signal for HIV activation. HIV infection in HC69.5 cells was assessed by the expression of GFP + cells. To activate the infection, we added 100 µg/ml of Poly IC following previous work published by Alvarez-Carbonell et al.12 (link),29 (link). Cells were also treated with Δ(9)-THC or CBD at two concentrations (0.01 µM and 1 µM). Cells were collected after 24 h of treatment, fixed, and permeabilized using the Fixation and Permeabilization Solution Kit (BD; Cat. No. 554715). Immortalized human microglial cells (C20, donated by Dr. Karn’s Lab)12 (link),29 (link) were used as uninfected and untreated control. Cells were acquired on an Accuri C6 flow cytometer (BD Accuri; Ann Arbor, MI; Dr. Alejandro Barbieri’s lab, FIU) and analyzed with FlowJo software (Tree Star, Inc.; Ashland, OR). Gating strategy: Forward and side scatter density plots were used to identify interested cell population and to exclude debris. Doublets were excluded by Forward scatter height vs. forward scatter area density plot. Single-parameter histograms were used to identify GFP-positive cells transferring the gate from unactivated cells. Results were expressed as numbers of positive cells.
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9

Insulin-positive and -negative cell sorting

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Human pancreatic islets of non-diabetic subjects were cultured with standard medium, or in the presence of IGFBP3 for 72 h as previously described (see “Pancreatic islets and Interventional studies”), and dissociated by trypsinization. In order to select insulin-positive and -negative populations, the cell fraction obtained was permeabilized using the Fixation and Permeabilization Solution Kit (554714, BD Biosciences) and stained with an APC-conjugated anti-insulin antibody (1:100, IC1417A, R&D Systems). Stained cells were flow-sorted using MoFlo Legacy (Beckman Coulter, Brea, CA) and analyzed by qRT-PCR.
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10

Intracellular TNF-α Expression Analysis

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Intracellular TNF-α expression was analyzed using a Fixation and Permeabilization Solution Kit with BD GolgiPlugTM (BD Bioscience). Briefly, THP1 monocytes (1 × 105 cells/ml) or macrophage-like cells (about 2.0 × 105 cells/ml) were exposed to X-rays. At 24 h after X-irradiation, LPS (1 μg/ml) or FSL-1 (50 ng/ml) was added to cultures, and the cells were cultured for an additional 8 h. GolgiPlug, which inhibits protein transporters, was added to the culture medium after 2 h of an 8-h culture. Cells were harvested and fixed using Cytofix/CytopermTM solution (BD Bioscience) for 15 min on ice. After washing twice in Perm/WashTM solution (BD Bioscience), cells were suspended in Perm/WashTM solution and were stained with anti-human TNF-α-FITC mAbs or isotype control at room temperature in the dark. After 30 min, the cells were washed with Perm/WashTM solution and were analyzed using a flow cytometer.
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