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12 protocols using cd3 apc fire750

1

Zika Virus Detection in Immune Cells

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Cells were fixed with paraformaldehyde (PFA) and treated with either BSA (extracellular staining) or BSA/Saponin to measure intracellular staining. The following antibodies were used to detect Zika virus: anti-Flavivirus 4g2 mouse IgG2a (NovusBio), anti-Flavivirus 4g2 monoclonal rabbit (Absolute Antibody), anti-Zika virus monoclonal Rabbit (Genetex).
All other antibodies were anti-human: DC-SIGN mouse IgG1 (AZN-D1), anti-langerin mouse IgG1 (10E2) both in house made, PE conjugated CD207 (langerin), APC conjugated CD1a (BD Biosciences), CD86-FITC (BD Pharmingen), CD80-PE (BD Pharmingen), CD83-APC (BD Pharmingen), DC-SIGN-FITC (R&D systems), CD3-APC/Fire750 (Biolegend), CD11c-APC (Biolegend), PEcy7-HLA-DR (BD Pharmingen), APCcy7-CD14 (BD Biosciences), APCcy7-CD11c (Biolegend),APC-AXL (Thermofisher, PE-MerTK (Thermofisher) and anti-Tyro3 (Thermofisher). For secondary detection the following antibodies were used: AF488-conjugated goat anti-mouse IgG2a (Invitrogen), AF647-conjugated donkey anti-rabbit (Thermofisher), FITC-conjugated goat-anti-mouse IgM (Invitrogen), AF488-conjugated donkey anti-rabbit (Thermofisher).
Flow cytometric analyses were performed on a BD FACS Canto II (BD Biosciences) and data was analysed using FlowJo V10 software (TreeStar).
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2

Multiparameter Immune Cell Profiling

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PBMCs were stained with the following antibodies: CD3-APC/Fire750 (BioLegend), CD14-APC/Fire750 (BioLegend), CD20-APC/Fire750 (BioLegend), CD56-APC (Tongsheng Shidai) and CXCR5-BV421 (BD Biosciences). Data were acquired using an Amnis ImageStreamX Mark II Imaging Flow Cytometer (Amnis, Seattle, WA, USA) and analyzed using the Amnis IDEAS software v6.2 (Amnis).
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3

Comprehensive Immune Profiling by Flow Cytometry

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Cells were washed with PBS and stained first with LIVE/DEAD stain followed by combinations of cell surface markers, including: CD3 APC-Fire750, CD4 PE-CF594, CD8 PerCP-Cy5.5, CD45RA PE-Cy7, CD27 APC, PD-1 PE, CD39 BB515, CCR7 BV421 (all BioLegend), TIGIT-BV421, CD57-BB515 (BD Biosciences). For staining of transcription factors surface Foxp3 Transcription Factor Staining Buffer (Invitrogen) was used, according to manufacturer’s instructions, to fix and permeabilize cells before staining with T-bet-BV786 (BD Biosciences) and Eomes-PE-eFluor 610 (Invitrogen). Samples were fixed with 2% PFA, acquired on either a CyAn (Beckman Coulter) or LSR Fortessa (BD Biosciences) flow cytometer and analysed using FlowJo v9.9.6 software (FlowJo, Ashland, OR, USA).
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4

Characterization of Infiltrating T-cell Subsets

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Transplanted aortas were harvested 3 weeks posttransplantation. Leukocytes were retrieved from the aorta as previously described.18 Briefly, harvested aortas were digested in a phosphate‐buffered saline solution with 450 U/mL collagenase type I, 125 U/mL collagenase type XI, 60 U/mL hyaluronidase type I‐S, and 60 U/mL deoxyribonuclease I for an hour at 37°C. After passing through a 70 µm cell strainer, cell suspension was stimulated O/N with Phorbol 12‐myristate 13‐acetate (Sigma, St. Louis, MO) 10 ng/mL and Ionomycine (EMD Millipore, Burlington, MA) 1 µg/mL O/N at 37°C followed by Brefeldine A (Sigma) 5 µg/mL treatment for 3 hours at 37°C. Infiltrating T cells subsets were characterized using CD3 APC/Fire750 (Biolegend, San Diego, CA), anti‐TCR gamma delta (TCRγδ) (clone GL3), BV421 (BD Biosciences), TCR beta (TCRβ) chain (clone: H57‐597), Alexa Fluor 488 (BD Biosciences), transcription factor retinoic acid receptor‐related orphan receptor gamma (RORγ) PerCP‐efluor 710 (eBioscience, San Diego, CA), IL‐17A BV711 (Biolegend), and IL‐17F Alexa fluor 647 (Biolegend) antibody staining. Samples were run on a flow cytometer (FACScan, Becton Dickinson) and analyzed on the computer software FlowJo.
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5

Comprehensive Immune Cell Profiling

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The cells were extracted from lymph nodes, spleen, or colon tissue digested by collagenase. Isolated cells were stained with following antibodies: CD8-PE-CY7 (Thermo Scientific), CD4-APC-Fire™ 750 (BioLegend), IFN-γ-FITC (BioLegend), IL-17-APC (BioLegend), FOXP3-PE (BioLegend), CD19-PE (BioLegend), NK1.1-FITC (BioLegend), CD11B-APC (BioLegend), Gr-1-FITC (BioLegend), F4/80-PE (BioLegend), CD11C-APC-CY7 (BioLegend), MHC-II-PE/Dazzle™ 594 (BioLegend), CD8-APC (BioLegend), Ki67-PerCP-CY5.5 (BioLegend), Annexin V-FITC (BioLegend), CD103-PE (BioLegend), CD69-PE-CY7 (BioLegend), CD44-PE-CY7 (BioLegend), CD62L-FITC (BioLegend), CD107-FITC (BioLegend), IFN-γ-APC (BioLegend), CD107-PE (BioLegend), IFN-γ-PE (BioLegend), CD3-FITC (BioLegend), CD3-APC/Fire™ 750 (BioLegend), CD8-APC (BioLegend), IFN-γ-PE-CY7 (BioLegend), CD69-APC/Fire™ 750 (BioLegend), Tetramer-SIINFEKL-PE (MBL), p-JNK-PE (Cell Signaling Technology), p-IRAK4-Alexa Fluor 488 (Cell Signaling Technology). Intracellular staining was carried out using the Cytofix/Cytoperm kit (BD Pharmingen) following a 4 h restimulation by PMA/ionomycin (Sigma) in the presence of GolgiPlug (BD Pharmingen). Flow cytometric data acquisition was performed on a NovoExpress flow cytometer and analyzed with NovoExpress software (ACEA Biosciences).
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6

Multiparametric Flow Cytometry of Lymphocytes

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Collection and preparation were previously described (12 (link)). Red blood cells were lysed using ice-cold deionized water for 30 s. White blood cells were then resuspended in FACs buffer [1× phosphate buffered saline (PBS), 2% heat-inactivated fetal bovine serum (FBS)], counted, and blocked for 10 min in FACS Buffer and Human Trustain FcX Fc receptor blocking solution (Biolegend; #422302) at room temperature, followed by staining with CD3-APC/Fire750 (BioLegend; #344840), CD56-PE (BioLegend; #318306), CD8-PerCP (BioLegend; #344708), CD11a-PE/Cy7 (BioLegend; #301220), CD16-FITC (BioLegend; #302006), CD69-APC (BioLegend; #310910). The corresponding immunoglobulin G (IgG) isotype controls were used for staining the lymphocytes. Cells were analyzed on a BD FACSCanto™ II, and the FACs data were analyzed using FlowJo V.10 data analysis software.
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7

Murine Lymphoid Tissue Immunophenotyping

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Mesenteric lymph nodes and spleen samples were washed and conserved in complete RPMI (10 % FCS). Samples were first grinded on a nylon mesh (40 μm cell strainer, Greiner), and large debris was removed. Cell suspensions were filtered through a 70 μm mesh (Miltenyi Biotec) and centrifuged at 4 °C, 600 xg, for 5 min. Cell suspensions were then washed and resuspended in phosphate-buffered saline (PBS) supplemented with 2% bovine serum albumin (BSA) for counting on an automated cell before direct cell surface staining. For intracellular staining, cells were fixed and permeabilized with a commercially available fixation/permeabilization kit (eBioscience). Single-cell suspensions were stained with antibodies to the following markers: CD45-BV421, CD3-APC/Fire750, CD4-FITC, CD25-BV510, CD8a-BV711, CD335-PECy7, CD19-BV605, CD11b-PERcpCY5.5, RORγt-APC, and Foxp3-PE in presence of FCBlock CD16/32; all antibodies were obtained from Biolegend. The gating strategy is detailed in Supplementary Figure 8. Gallios cytometer (Beckman) was used for cell acquisition, and the flow cytometry data were analyzed with Kaluza software.
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8

In Vitro Blood-Brain Barrier Migration

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Transmigration was assessed using the hCMEC/D3 cell line as an in vitro model of human blood-brain barrier (Merck Millipore). The day before migration experiments, 3 × 105 endothelial cells were seeded on a collagen-coated 3 μm pore size transwell (Falcon; Corning, Corning, NY) in EndoGRO medium (Merck Millipore, Burlington, MA) as previously described.21 (link) PBMCs were stained with the following antihuman antibodies: CD4-PE, CD8-FITC (Beckman Coulter), and CD3-APC/Fire 750 (Biolegend, San Diego, CA). CD3+CD4+CD8 T cells were sorted using an FACS Aria II (BD Biosciences). Then, 5 × 105 CD4+ T cells in complete Roswell Park Memorial Institute medium supplemented with 10% of fetal bovine serum were added in the upper chamber of a transwell. After 20 hours at 37°C, migrated and nonmigrated cells were collected. For both compartments, cells were stained as described earlier and analyzed by flow cytometry (FACS Celesta; BD Biosciences).
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9

Flow Cytometry Analysis of Immune Cells

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Blood samples for flow cytometry analysis were collected into TransFix/EDTA Vacuum Blood Collection Tubes during monotherapy on days 1 and 5, pre and 4 hours post (AE2 hours) BL-8040 administration, and during the combination period at the end of cycle 1, day 15 and at the end of cycle 2, day 21. Cells were stained with antibody panels for 30 minutes at room temperature in the dark followed by red cell lysis using lysing solution (BD Biosciences; 15 minutes) and washing. Antibody panels included CD45 (2D1, BD Biosciences), CD3 (APC/Fire-750, BioLegend), CD4 (RPA-T4, Bio-Legend), CD8 (SK1, BioLegend), CD19 (HIB19, BioLegend), CD56 (NKH-1, Beckman Coulter), and CD38 (HB7, BioLegend) were used for the assessment of T helper cells (CD3 CD4), cytotoxic T cells (CD3 CD8), activated T cells (expressing upregulated levels of CD38), NK cells (CD3 À CD56 þ ), NKT cells (CD3 þ CD56 þ ), and B cells (CD3-CD19 þ ). Stained cells were acquired on FACSLyric flow cytometer (BD Biosciences) and analyzed using FlowJo version 10.
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10

Quantification of DNA Damage in T Cells

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The following monoclonal antibodies were purchased from BioLegend: anti-γH2AX-Alexa 488, Annexin V-FITC, CD3-APC/Fire750, CD4-APC, CD8-APC/Fire750, and CD279 (PD-1)-PE.
Immuno uorescence detection of γH2AX nuclear foci CD3+ T cells cultured in 24-well plates were collected in centrifuge tubes and washed twice with PBS. T cells were xed and permeabilized using a True-Nuclear™ Transcription Factor Buffer Set (BioLegend, USA). T cells were then incubated for 30 min with PBS containing 1% BSA and an anti-γH 2 AX antibody conjugated to Alexa 488 at RT. T cells were washed thrice with PBS and counterstained with DAPI. The immunostained cells were subjected to ow cytometry analysis and confocal laser scanning microscopy (FLUOVIEW FV10i-DOC, OLYMPUS, Japan). BD FACS Canto II (BD Biosciences, USA) was used to measure the forward scatter, side scatter, and expression levels of γH2AX nuclear foci. Data were analyzed using the Flowing Software (Turku Bioscience, Finland).
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