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7 protocols using anti tnf apc

1

Multiparametric Analysis of EBV-Specific T Cells

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For analysis of LMP1&2-specific and EBNA1-specific T-cell frequencies, AdE1-LMPpoly-expanded products were stimulated for 4 hours in the presence of GolgiPlug (BD Biosciences) with a pool of defined epitopes from LMP1&2 or EBNA1 or with an overlapping set of peptides encompassing the whole EBNA1 protein (all from Mimotopes, GenScript or JPT Technologies), and then assessed for the intracellular production of IFN-γ. For multiparametric analysis, cells were stimulated for 4 hours in the presence of GolgiPlug and GolgiStop (BD Biosciences) with the peptides listed above and anti-CD107a-FITC (BD Biosciences). Cells were then washed and stained with anti-CD8-PerCPCy5.5 (eBioscience) and anti-CD4-PECy7 (BD Biosciences), fixed and permeabilised with Cytofix/Cytoperm (BD Biosciences), washed again and stained with anti-IFN-γ-AF700, anti-IL-2-PE and anti-TNF-APC (all from BD Biosciences). After a further wash, cells were resuspended in PBS and acquired using a BD LSR Fortessa with FACSDiva software (BD Biosciences). Post-acquisition and Boolean analysis was performed using FlowJo software (TreeStar).
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2

Allogeneic CD8+ T Cell Proliferation

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To study CD8+ T cell proliferation and functionality, 5000 DCs were stimulated as indicated and co‐cultured with 20 000 allogeneic naïve CD8+ T cells (CD8+, CD27+, CD45RO, and CD45RA+) in the presence of 1 pg/mL Staphylococcus aureus enterotoxin B (SEB; Sigma–Aldrich). To determine proliferation, CD8+ T cells were incubated with 0.5 μM CFSE (Invitrogen) and washed extensively prior to co‐culture. At day 3 or 4, cells were incubated overnight with the modified thymidine analogue EdU (Click‐iT kit; Invitrogen) and further processed according to the manufacturer's instructions. The percentage of divided cells (EdU+ or CFSE) was determined by flow cytometry (Canto II, BD Biosciences). To determine intracellular granzyme B expression, cells were harvested at day 4 or 5, washed with PBS, fixated with 4% formaldehyde (Sigma–Aldrich) for 15 min, washed again, permeabilized with 0.5% saponin (Calbiochem) in PBS containing 0.5% BSA (PAA) and 0.1% sodium azide (Merck), and stained with anti‐granzyme B‐PE (Sanquin Blood Supply) and analyzed by flow cytometry. For intracellular IFN‐γ or TNF staining, CD8+ T cells were restimulated at day 4 or 5 with 100 ng/mL PMA, 1 μg/mL ionomycin, and 10 μg/mL brefeldin A (all Sigma–Aldrich) for 6 h, washed, fixated, and permeabilized as described above, stained with anti‐IFN‐y‐ FITC and anti‐TNF‐APC (both BD Biosciences) and analyzed by flow cytometry.
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3

Activation of Sorted CD8+ T Cells

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Sorted CD8+CD44lo T cells stimulated at 2 x 104 cells per well in mAb-coated 24-well plates for up to 72 hours (h) were incubated in the presence of 10 U/mL recombinant human IL-2 (Roche Diagnostics, Mannheim, Germany). The mAb were coated onto Nunc plates overnight in PBS at the following concentrations: anti-CD3ε (clone 145-2C11) at 10 μg/mL; anti-CD8α (clone 53–6.7) at 10 μg/mL; anti-CD11a (clone I21/7.7) at 5 μg/mL; anti-CD28 (clone 37.51) at 10 μg/mL [16 (link)]. To permit intracellular cytokine staining, GolgiPlug at a 1:1000 dilution (BD Biosciences, San Diego, CA, USA) was added for the last 5 h of the incubation. After incubation, cells were surface-stained using anti-CD8α-PE (BD Pharmingen; clone 53–6.7), fixed and permeabilised using Cytofix/Cytoperm buffer and 1 × Perm/Wash buffer (BD Biosciences) according to manufacturer’s instructions and stained with anti-IFNγ-FITC (BD Pharmingen; clone XMG1.2) and anti-TNF-APC (BD Pharmingen; clone MP6- XT22) [17 (link)]. Cells were then acquired using FACSCalibur flow cytometer (BD Biosciences) and data were analyzed by using FlowJo software (Versions 9&10) (FlowJo LLC, Ashland, Oregon).
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4

T Cell Cytokine Response to SARS-CoV-2 Antigens

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Cultured T cells were stimulated with individual SARS‐CoV‐2 antigen overlapping peptide pools and incubated for 4 h in the presence of GolgiPlug, GolgiStop and anti‐CD107a‐FITC (BD Biosciences). Following stimulation, cells were washed and stained with anti‐CD8‐PerCP‐Cy5.5 (eBioscience) and anti‐CD4‐PE‐Cy7 or anti‐CD4‐Pacific Blue (BD Biosciences) for 30 min before being fixed and permeabilised with BD Cytofix/Cytoperm solution (BD Biosciences). After 20 min of fixation, cells were washed in BD Perm/Wash buffer (BD Biosciences) and stained with anti‐IFN‐γ‐Alexa Fluor700, anti‐IL‐2‐PE and anti‐TNF‐APC (all from BD Biosciences) for a further 30 min. Finally, cells were washed again and acquired using a BD LSRFortessa with FACSDiva software. Postacquisition analysis was performed using FlowJo software (TreeStar). Cytokine detection levels identified in the no‐peptide control condition were subtracted from the corresponding test conditions to account for nonspecific, spontaneous cytokine production.
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5

Multifunctional SARS-CoV-2 T Cell Profiling

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Cultured T cells (5 × 105 per test) or PBMC (2 × 106 per test) were stimulated separately with the SARS-CoV-2 overlapping peptide pools (1 µg/mL of each peptide), individual defined epitopes (1 µg/mL) or with a cytokine stimulation cocktail (eBioscience), and incubated for 4 h (T cells) or 6 h (PBMC) at 37 °C in the presence of GolgiPlug (Brefeldin-A), GolgiStop (Monensin) and anti-CD107a-FITC (BD Biosciences). Following stimulation, cells were washed and stained with anti-CD8-PerCP-Cy5.5 (eBioscience), anti-CD4-Pacific Blue (BD Biosciences) and live/dead fixable near-IR dead cell stain (Life Technologies) for 30 min at 4 °C before being fixed and permeabilized with Fixation/Permeabilization solution (BD Biosciences). After 20 min of fixation, cells were washed in BD Perm/Wash buffer (BD Biosciences) and stained with anti-IFN-γ-Alexa Fluor 700, anti-IL-2-PE and anti-TNF-APC (all from BD Biosciences) for a further 30 min at 4 °C. Finally, cells were washed again and acquired using a BD LSRFortessa with FACSDiva software. Post-acquisition analysis was performed using FlowJo software (TreeStar). Cytokine levels detected in the no-peptide control condition were subtracted from the corresponding test conditions to account for non-specific, spontaneous cytokine production.
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6

Comprehensive Immunophenotyping of SARS-CoV-2-Specific T Cells

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Cultured T cells were stimulated separately with the SARS-CoV-2 overlapping peptide pools, corresponding to ORF3a, N, M and S proteins from SARS-CoV-2, and incubated at 37°C for 4 hours in the presence of GolgiPlug. Following stimulation, cells were washed and stained with anti-CD8-BV786, anti-CD4-PE-Cy7, anti-CD27-PE/Dazzle 594, anti-CD28-BV480 (BD Biosciences), anti-CD57-BV605, anti-CD45RA-FITC (BD Biosciences) and live/dead fixable near-IR dead cell stain (Life Technologies) for 30 minutes at 4°C before being fixed and permeabilized with TF Fix/Perm buffer (BD Pharmingen). After 1 hour of fixation, cells were washed in TF Perm/Wash buffer (BD Pharmingen) and stained with anti-TNF-APC (BD Biosciences), anti-Tbet-PE (eBioscience), anti-Eomes-PerCP-eFluor 710 (eBioscience), anti-Granzyme B-AF700 (BD Biosciences) and anti-Perforin-BV421 (Biolegend) for a further 30 minutes. Finally, cells were washed again and acquired using a BD LSRFortessa with FACSDiva software. Post-acquisition analysis was performed using FlowJo software (TreeStar). Gating analysis for the detection of antigen-specific TNF-producing cells is outlined in S1 Fig. TNF-producing cells from positive assays were then concatenated and t-SNE analysis was performed using the following parameters (Eomes, T-bet, CD27, CD28, CD57, granzyme B and perforin).
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7

SARS-CoV-2 Reactive T Cell Profiling

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Cultured T cells were stimulated separately with the SARS-CoV-2 overlapping peptide pools and incubated for 4 hours at 37°C in the presence of GolgiPlug, GolgiStop and anti-CD107a-FITC (BD Biosciences). Following stimulation, cells were washed and stained with anti-CD8-PerCP-Cy5.5 (eBioscience), anti-CD4-Pacific Blue (BD Biosciences) and live/dead fixable near-IR dead cell stain (Life Technologies) for 30 minutes at 4°C before being fixed and permeabilized with Fixation/Permeabilization solution (BD Biosciences). After 20 minutes of fixation, cells were washed in BD Perm/Wash buffer (BD Biosciences) and stained with anti-IFN-γ-Alexa Fluor 700, anti-IL-2-PE and anti-TNF-APC (all from BD Biosciences) for a further 30 minutes at 4°C. Finally, cells were washed again and acquired using a BD LSRFortessa with FACSDiva software. Post-acquisition analysis, including t-distributed stochastic neighbor embedding (t-SNE), was performed using FlowJo software (TreeStar). Cytokine detection levels identified in the no-peptide control condition were subtracted from the corresponding test conditions to account for non-specific, spontaneous cytokine production. T cells were deemed reactive to an antigen if >1% of CD4+ or CD8+ T cells produced IFN-γ after subtraction of background.
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