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19 protocols using ifn γ fitc

1

Multicolor Flow Cytometry of Immune Cells

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The CD8+ T cells were incubated with IFN‐γ‐FITC (11‐7311‐41, Invitrogen), anti‐human CD8‐APC (#344721, BioLegend), or anti‐mouse CD8a‐APC (17‐0081‐82, Invitrogen), and TAMs were incubated with F4/80‐FITC (#23107, BioLegend) and Arg‐1‐APC (IC5868A, R&D Systems) in the dark for 30 min. The phenotype of CD8+ T cells and TAMs was then analyzed by flow cytometry.
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2

Detailed Cell Staining and Analysis

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Cell suspensions were made and cells stained as described (25 (link), 37 (link)) using the following directly conjugated antibodies from BioLegend unless otherwise stated: CD11b APC (clone M1/70), Siglec-F PE (BD Bioscience, clone E50-2440), CD4 FITC, AF700 (clone GK1.5), ST2 APC (clone DIH9), CD117 APC (ACK2), FcεRI PerCP-eFluor 710 (eBioscience, clone MAR1), CD49b PE (clone DX5), IL4rα PE (clone I015F8), and CD25 (clone 3C7). A minimum of 1 × 105 cells were acquired, and doublets were excluded by gating cells on FSC-H/FSCA, as illustrated in Supplementary Figure 1. For intracellular cytokine staining, mLN cells were stimulated with Cell Activation Cocktail (with Brefeldin A, BioLegend) at 1 × 106 cells/ml, incubated in complete RPMI (10% FBS and 5% Pen/Strep) at 37°C for 6 h. Then, cells were fixed using Ic Fixation buffer (Invitrogen) and permeabilized using Permeabilization Buffer (Invitrogen) to carry out the intracellular staining for IL-4 PE (clone 11B11), IL-13 Pecy7 (Invitrogen, clone eBio13A), and IFN-γ FITC (clone XMG1.2). Cells (2 × 106) were used for transcription factor staining. Staining against Foxp3 PE and Gata3 PE was performed using the Transcription Factor Staining Buffer Set according to the manufacturer’s instructions. Data were acquired on a C6 Accuri flow cytometer (BD Biosciences) or Cytoflex (Beckman) and analyzed using FlowJo v10.6.
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3

FACS Analysis of Myeloid-Derived Suppressor Cells

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Cells were stained with specific antibodies or control isotypes using conventional protocols. The following anti-mouse antibodies were used for FACS analysis of MDSCs: CD11b/PECy5, Gr1/PE, Gr1/APC, CD62L/FITC, F4/80/FITC, CD11c/PE, and MHC CI OVA peptide/Biotin from eBiosciences (San Diego, CA); as well as CD124/PE, CD40/FITC, CD86/FITC, IA-IE/FITC, Ly6C/FITC and Ly6G/PE that were purchased from BD Biosciences (San Jose, CA). Lymphocytes characterization was performed with the next specific antibodies: CD8/PE and CD8/Biotin, CD69/PECy5, CD62L/FITC, CD247/PE, CD4/PE, CD4/PECy5, CD25/PECy5, Foxp3/Biotin, IFN-γ/FITC, IL-4/PE and IL-17/PE, all from eBiosciences. FITC-conjugated Streptavidin was purchased also from eBiosciences. In all cases, cells were previously incubated with anti-mouse FcγR 2.4G2 ascites (HB-197; ATCC) to reduce the non-specific binding. For intracellular staining, cells were fixed and permeabilized, according to the manufacturer’s protocol, with either Foxp3 Staining Buffer Set or IC Fixation and 10X Permeabilization Buffers from eBiosciences. Cells were acquired using both FACScan (BD Biosciences) and Gallios (Beckman Coulter, Miami, FL) flow cytometers and analyzed with Kaluza 1.2 (Beckman Coulter) and FlowJo 5.7.2 (Tree Star Inc., USA) softwares.
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4

PBMC Expansion and Cytokine Analysis

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The predicted peptides were synthesized (Genscript Corporation). PBMCs were cultured in complete RPMI (Core Media Preparation Facility MSKCC) with peptides at 1 μg/mL, peptide vehicle (DMSO, Sigma-Aldrich) and CEF peptide pool (2 μg/ml, C.T.L) for 21 days with peptide restimulation at day 7 and day 14. IL-2 (Proleukin, Chiron) and IL-15 (Peprotech, cat#200-15) were added every 3 days at 10 IU/mL and 10 ng/mL respectively. Intracellular Cell Staining (ICS) was performed at day 14, and day 21 after 6 hr re-stimulation in the presence of monensin for 5 hr (GolgiStop, BD). Cells were then stained for 15 min with viability dye (LIVE/DEAD Fixable Aqua Dead Cell Stain Kit, ThermoFisher) at 4°C followed by 30 min incubation with CD45-APC-H7 (BD PharMingen, clone 2D1), CD3-Pacific Blue (BD PharMingen, clone UCHT1), CD4-PerCP-Cy5.5 (eBioscience, clone OKT4), CD8-PE (BD Biosciences, clone SK1). Cells were then fixed and permeabilized with BD Cytofix/Cytoperm (BD Biosciences) for 20 min at 4°C and washed with BD Perm/Wash (BD Biosciences). The ICS was performed in BD Perm/Wash with IFN-γ-FITC (eBioscience, clone GZ-4) and TNF-α-PE-Cy (eBioscience, clone MAb11) at 4°C for 30 min. Samples were acquired on a BD LSRII flow cytometer (BD Biosciences) and the analysis was performed on FlowJo software (FlowJo, LLC).
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5

Flow Cytometry Immunophenotyping Protocol

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For flow cytometry, the following fluorochrome-conjugated monoclonal antibodies were used. BD Biosciences: HLA-DR-APC (Clone: G46-6), CD86-FITC (Clone: FUN-1), CD80-PE (Clone: L307.4), CD54-APC (Clone: HA58), CD25-FITC (Clone: M-A251), CD127-BV421 (clone HIL-7R-M21), IFN-γ-FITC (Clone: 4S.B3), IL-4-PE (Clone: MP4-25D2); eBioscience: FoxP3-APC (Clone: 236A/E7), IL-17A-PE (Clone: Ebio64cap17); Beckman Coulter: CD40-PE (Clone: MAB89); Biolegend: CD4-PerCP (Clone: SK3). Cell viability was detected using the fixable viability dye eFluor 506 (eBioscience).
Antigen affinity-purified polyclonal anti-human TLR4 goat IgG was purchased from R&D systems. Cytokines (recombinant human granulocyte-macrophage colony-stimulating factor and IL-4), MicroBeads (CD14 and CD4) and cell purification units were obtained from Miltenyi Biotec. Protein-A agarose beads were from Cell Signalling Technology, and E. coli 055:B5 LPS and Polymyxin B-conjugated agarose beads were from Sigma-Aldrich. TLR4 signaling inhibitor CLI-095 and CpG ODN 2006 were procured from InvivoGen.
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6

Intracellular Cytokine Staining Assay

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Cells were stained for intracellular cytokine secretion after 14 days in culture. 200,000 cells were pulsed with individual peptides or the pool of peptides at 10μg/ml for 5 hours, with 10μg/ml Brefeldin A (eBiosciences) added after the first hour to prevent cytokine secretion into the supernatant. Cells were washed and stained for the surface markers CD8 APC-H7, CD4 PerCP, and CD3 V500 (BD) together with LIVE/DEAD viability marker (Invitrogen) diluted in PBS for 30 minutes on ice, then washed and fixed with fixation solution (eBioSciences) for a further 30 minutes on ice or left overnight at 4°C. Cells were permeabilised by washing with permeabilisation buffer (eBioSciences) and stained with the intracellular antibody IFNγ FITC (eBiosciences) diluted in the permeabilisation buffer for 30 minutes on ice. Cells were washed with PBS and resuspended in FACS buffer for acquisition by flow cytometry. The presence of CD107 on the T cell surface was assessed by the addition of PE conjugated CD107 (BD) antibody at the same time as Brefeldin A. CD4+ and CD8+ T cell responses to the peptide diluent DMSO were negligible and below 0.001%.
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7

Single-Cell Isolation and Analysis of Lymph Node

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To obtain single-cell suspension, the bilateral cervical draining lymph nodes (DLNs) were minced between the frosted ends of two glass slides in the media containing RPMI-1640 (WelGENE, Daegu, Korea) and 10% fetal bovine serum (Gibco, Grand Island, NY, USA) and were then filtered through a cell strainer. The resultant single-cell suspensions were stained with fluorescence-conjugated antibodies against CD4-PE cy7 eBioscience, Waltham, MA) and IFN-γ-FITC (eBioscience). For intracellular IFN-γ staining, the cells were prestimulated for 5 h at 37 °C with 5 μg/mL anti-CD3 (BD Pharmingen, San Diego, CA) and 5 μg/mL anti-CD28 (BD Pharmingen) in the presence of Cell Stimulation Cocktail including phorbol 12-myristate 13-acetate (PMA) and ionomycin (Cat No. 00-4970, eBioscience). The stained cells were assayed by a flow cytometer (S1000EXi Flow Cytometer, Stratedigm, San Jose, CA, USA) and were analyzed using FlowJo.
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8

Multiparameter Analysis of Memory T Cells

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Memory CD4+ T cells were stimulated with phorbol 12-myristate acetate (PMA) (50 ng/mL) and ionomycin (1 µg/mL) for about 10 hours, with the last 4 hours with 10 µg/mL Brefeldin A and 2 µM monensin at 37°C and 5% CO2. In some instances, cells were first treated with CSA (1 µM) for 1 hour before PMA/Ionomycin treatment. After 10 hours, cells were fixed and permeabilized with the Foxp3 staining kit (eBioscience, San Diego, CA), according to the manufacturer's protocol. The following antibodies were used: interferon-γ (IFN-γ) FITC, interleukin (IL) 17–Alexa Fluor 647, tumor necrosis factor α (TNFα)–Alexa Fluor700, Granulocyte Macrophage Colony Stimulating Factor (GM-CSF) PECF594, IL-2 BV510, IL-10 PE, Foxp3 APC, RORγc PE, and PD1 BV605 (all eBioscience). Stained cells were acquired by CytoFLEX S (Beckman Coulter) and analyzed with the CytExpert Software.
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9

Multiparametric Flow Cytometry for T-cell Profiling

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Single cell suspensions were isolated from tissues and stained with fluorescence-conjugated antibodies against CD4-PE cy7 (Cat# 25-0041, eBioscience, Waltham, MA), IFN‐γ-FITC (Cat# 11-7311, eBioscience), and IL-17-APC (Cat# 17-7177, eBioscience). The stained cells were assayed by a flow cytometer (S1000EXi Flow Cytometer, Stratedigm, San Jose, CA) and analyzed using FlowJo program (Tree Star, Inc., Ashland, OR).
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10

Profiling Memory CD4+ T Cells

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Frozen PBMCs obtained from the patient and two healthy donors were thawed when cells (106) were either unstimulated or stimulated with PMA (20ng/mL; Sigma) and ionomycin (1μM; Sigma) in the presence of brefeldin A (10μg/mL; Sigma) at 37°C overnight. For detection of intracellular cytokines, cells were stained with Live/Dead Fixable Yellow Dead Cell Stain Kit (Invitrogen) as well as for extracellular CD3 (eVolve605), CD8 APC-eFluor780 (eBioscience), CD45RO PE-CF594 (BD Biosciences), and CD27 BV421 (BioLegend) for 30 min. Cells were fixed (paraformaldehyde 4%), permeabilized, and stained for intracellular antigens with CD4 PE-Cy7 (BD Biosciences), IL-17A PE, IFN-γ FITC, and TNF-α APC (eBioscience). Data were collected using an LSR Fortessa (BD Biosciences) and analyzed using FlowJo software (Treestar) by gating on lymphocytes (forward & side scatter) and on viable CD3+CD4+CD8-CD45RO+ CD27− cells.
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