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52 protocols using anti cd3 pe cy7

1

Quantifying γδ T Cell Responses

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Single-cell suspensions were prepared from cultured cells or fresh tumor tissues. Red cells were removed using ammonium chloride lysis buffer when necessary. 1 × 106 cells were incubated at 4°C for 30 min with different combinations of fluorescent-conjugated antibodies for γδ T cells (anti-Vγ9 TCR-allophycocyanin [BioLegend, San Diego, CA, USA], anti-CD3-PECy7 [BioLegend], anti-Vδ2 TCR-peridinin chlorophyll [PerCP]-Cy5.5 [BioLegend], and anti-Vδ1 TCR-FITC [Thermo Fisher Scientific]), T cells (FITC-anti-CD4 [BD Biosciences, San Jose, CA, USA], PE-anti-CD8 [BD Biosciences], and PE/Cy7-anti-CD3 [BioLegend]). For intracellular staining of IFN-γ, cells were incubated with staphylococcal enterotoxin B for 6 hr in the presence of 19 brefeldin A as described by the manufacturer (BD Biosciences, San Jose, CA, USA). Cells were then stained with IFN-γ PerCP-Cy5.5 (BD Biosciences).
For γδTDE-mediated cell proliferation experiments, CD8+ T cells were stained with CFSE (4.5 mM) at 37°C for 20 min. The labeled cells were cultured in AIM V Medium with IL-2 and zoledronate at the presence of γδTDE derived from different conditions for 6 days. Cells were harvested, and CFSE was measured by a flow cytometer with 488 nm excitation and emission filters.
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2

Comprehensive Immunophenotyping of Dendritic Cells and T Cells

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For in vitro flow cytometry analysis, cells were harvested and incubated with Fixable Viability dye APC-eFluor 780 (1:1000 dilution, Ebioscience, San Diego, CA) for 20 min. For DC cultures, cells were then stained using directly conjugated antibodies against murine surface antigens, as follows: anti-CD40-PE, anti-CD80-FITC, anti-CD3-PE-Cy7, anti-CD11b-PE, anti-CD11c-APC, anti-CD86-Alexa Fluor 700, anti-CD8-BV605, and anti-MHCII-Percp-Cy5.5 (1:400 dilution, Biolegend, San Diego, CA) and analyzed with a BD LSR-Fortessa Flow Cytometer (Becton–Dickinson, Franklin Lakes, NJ). For OTI T cell analysis, flow cytometry panel was performed as described: anti-CD4-PE, anti-CD8-APC, anti-CD44-PErcp-Cy5.5, and anti-CD3 PE/CY7 (1:200, Biolegend). For ex vivo flow cytometry analysis, the directly conjugated antibodies against murine surface antigens are as follows: anti-CD3-Alexa Fluor 700 (1:50), anti-CD4-PE-Cy7 (1:100), anti-CD8-BV605 (1:100), anti-CD44-PE (1:200), and anti-CD62L-APC-Cy7 (1:100) for surface staining (Biolegend). For intracellular staining, cells were fixed/permeabilized stained using the Foxp3 staining kit (Ebioscience) using Foxp3-eFluor 450 (1:100, Ebioscience), granzyme B Alexa Fluor 647 (1:50, Biolegend) as described in the product specification sheet.
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3

Multiparameter Flow Cytometry of T-cell Subsets

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Purified CD8+ T cells, splenocytes and thymocytes were first stained for surface antigens and then treated with Foxp3 staining buffer set according to the manufacturer's directions (eBioscience). Anti-Eomes AlexaFluor 647 or eFluor 660 (Dan11mag, 1/75), anti-T-bet PE (eBio4B10, 1/100) and anti-CD49d FITC or PE (R1-2, 1/50) antibodies were purchased from eBioscience. Anti-CD8 PercP (53–6.7, 1/50), anti-CXCR3 APC (CXCR3-173, 1/50), anti-CD4 Pe-Cy7 (RM4-5, 1/100), anti-CD62L PE (1/100) or V450 (1/50) (MEL-14), anti-Bcl2 PE (3F11, 1/25), anti-Ki67 FITC (B56, 1/25), anti-CD44 FITC or V450 (IM7, 1/50), anti-CD127 Pe-Cy7 (SB/199, 1/50), anti-CD122 FITC (TM-BETA1, 1/50), anti-NK1.1 FITC (PK136, 1/50), anti-CD90.2 Pe-Cy7 (53-2.1, 1/100) and anti-IFNγ APC or PB or PE (XMG1.21/50) were purchased from BD biosciences. Anti-CD3 Pe-Cy7 (2C11, 1/100) was purchased from Biolegend.
In some experiments, brefeldin A (5 μg ml−1, Sigma) was added in samples for 3 h at 37 °C before intracytoplasmic staining. Blood samples were directly stained for surface antigens and then treated with FACS lysing buffer (BD biosciences) as described in the product data sheet. All samples were fixed with 1% paraformaldehyde in PBS prior to their processing using a Cyan flow cytometer (Dako Cytomation).
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4

Multiplexed Immunofluorescence Staining Protocol

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Formalin-fixed paraffin-embedded sections were rehydrated by immersing the slides in xylene for 4 minutes (twice), 100% ethanol for 2 minutes (twice), 95% ethanol for 2 minutes (twice), 80% ethanol for 2 minutes (twice), 70% ethanol for 2 minutes (twice), and PBS for 5 minutes (twice). Epitope retrieval was performed in IHC-Tek Epitope Retrieval Solution IW-1100 (IHC World, Ellicott, MD). The slides were blocked with 5% bovine serum albumin and stained with the following antibodies: PDK4 (Novus), p-PDHE1α, Ki-67, anti-CD4-PECy7, anti-CD3-PECy7 (all BioLegend), and goat antirabbit immunoglobulin G conjugated to Alexa Fluor 647 (A27040; Invitrogen, Carlsbad, CA).
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5

Comprehensive Immune Profiling by Flow Cytometry

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For in-vitro studies, the following flow cytometry panel was used in conjunction with CTV and viability dye: anti-CD3 Alexa700, anti-CD4 PE-Cy7, anti-CD8 APC, and anti-CD44 PE, all at a 1:200 dilution (Biolegend). For in-vivo and ex-vivo studies, the following flow cytometry panel was used: anti-CD3 PE-Cy7, anti-CD4 Pacific Blue, anti-CD8 APC, anti-CD44 PE, anti-CD62L APC-Cy7, and anti-CD25 Alexa 700, all at a 1:200 dilution, except anti-CD25 at a 1:50 dilution (Biolegend). Endogenous Foxp3 expression was detected either via eGFP of eYFP fluorescence, which is compatible with all panels but not when used with BODIPY-FL dye (493/503) or 2-NBDG (465/540). In those assays, Foxp3-based uptake of FA or Glucose was not performed, but all other cellular subsets described were tested. All acquisition was performed using a BD Fortessa flow cytometer (BD, MD, USA) at the Northwestern University Comprehensive Flow Cytometry core.
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6

Flow Cytometry Immunophenotyping Protocol

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For in-vitro studies the following flow cytometry panel was used in conjunction with CTV and viability dye: anti-CD3 Alexa700, CD4 PE-Cy7, CD8 APC, CD44 PE all at a 1:200 dilution purchased from Biolegend. For in-vivo and ex-vivo studies, the following flow cytometry panel was used: anti-CD3 PE-Cy7, CD4 Pacific Blue, CD8 APC, CD44 PE, and anti-CD25 Alexa 700 all at a 1:200 dilution (except anti-CD25 at a 1:50 dilution) and were purchased from Biolegend. Endogenous Foxp3 expression was detected via eYFP fluorescence (or re-stained with anti-Foxp3 Efluor-450 clone FJK-16 s for any overnight staining (Fisher)), all acquisition was performed using a BD Fortessa flow cytometer. For surface FA transporter measurement, anti-CD36-APC (Biolegend), SLC27A1 (sigma), and SLC27A4 was purchased from Abcam (Cambridge, UK), followed by secondary goat anti-rabbit IgG Alexa-647 (Jackson Immunoresearch, West Grove, PA). Proliferation was analyzed using both FACS DIVA software as well as FlowJo software to determine expansion indexes.
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7

Assessing NK Cell Activation in Cancer

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NCI-H1960, A549 and NCI-H1975 cells were seeded in 6-well plates, incubated overnight and treated with docetaxel and cisplatin (concentrations as described above). After 24 hours of treatment, the appropriate conditions were treated with human aCD70 or isotype control and co-cultured with NK cells at a 5:1 ratio. After washing, cells were stained with the following antibodies: anti-CD45 APC-Cy7 (1:50, Clone 2D1, Biolegend), anti-CD3 PE-Cy7 (1:100, Clone SK7, Biolegend), anti-CD56 PE-CF594 (1:25, Clone NCAM16.2, BD Biosciences), anti-CD69 PerCP-Cy5.5 (1:100, Clone FN50, Biolegend) and Live/Dead Fixable Aqua (1:50, Invitrogen) for 30 minutes at 4°C. Acquisition was performed on the Novocyte Quanteon (Agilent technologies).
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8

Flow Cytometry Immunophenotyping Protocol

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For in-vitro studies the following flow cytometry panel was used in conjunction with CTV and viability dye: anti-CD3 Alexa700, CD4 PE-Cy7, CD8 APC, CD44 PE all at a 1:200 dilution purchased from Biolegend. For in-vivo and ex-vivo studies, the following flow cytometry panel was used: anti-CD3 PE-Cy7, CD4 Pacific Blue, CD8 APC, CD44 PE, and anti-CD25 Alexa 700 all at a 1:200 dilution (except anti-CD25 at a 1:50 dilution) and were purchased from Biolegend. Endogenous Foxp3 expression was detected via eYFP fluorescence (or re-stained with anti-Foxp3 Efluor-450 clone FJK-16 s for any overnight staining (Fisher)), all acquisition was performed using a BD Fortessa flow cytometer. For surface FA transporter measurement, anti-CD36-APC (Biolegend), SLC27A1 (sigma), and SLC27A4 was purchased from Abcam (Cambridge, UK), followed by secondary goat anti-rabbit IgG Alexa-647 (Jackson Immunoresearch, West Grove, PA). Proliferation was analyzed using both FACS DIVA software as well as FlowJo software to determine expansion indexes.
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9

Comprehensive Immune Cell Profiling

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Stimulated cells were treated with GolgiPlug/Brefeldin A for the last 4 h of incubation to block secretion of cytokines. Cells were collected and transferred to a V-shaped 96-well staining plate, stained with the LIVE/DEAD Fixable Dead Cell Stain Kit-Aqua (Life Technologies) and Fc-receptors were blocked with 10% human serum. Next, extracellular surface markers were stained with anti-CD3-PECy7 (clone: SK7), CD4-PE (clone: RPA-T4) (both from BioLegend), CD8-APCH7 (clone: SK1), CD56-APC (clone: B159) (both from BD Biosciences) and pan-γδ TCR-FITC (clone: IMMU510) (Beckman Coulter). Cells were fixed/permeabilized with the Transcription Factor buffer set (BD Biosciences) followed by intracellular staining with IFN-γ-PerCPCy5.5 (clone: B27) (BD Biosciences). Stained cells were acquired using a FACSVerse instrument with the FACS Suite software (BD Biosciences). Lymphocytes were gated based on forward/side scatter properties. Viable lymphocytes were further gated on cell surface markers; NK cells were classified as CD3CD56+, T helper cells as CD3+CD4+, T cytotoxic cells as CD3+CD8+ and γδ T cells as CD3+γδ TCR+. Data was analysed using FlowJo Software (TreeStar).
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10

Multiparameter Flow Cytometry of Tumor-Infiltrating Lymphocytes

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Tumors were collected and processed into single-cell suspensions through digestion in collagenase type I (#2350118, Gibco) and Dnase I (#143582, Roche) at 37 °C for 45 min. After filtering with a 45 μm filter (BD Bioscience), the isolated cells were stained with the specific surface marker antibodies, anti-CD45-Percp-Cy5.5 (#103132; Biolegend), anti-CD3-PE-Cy7 (#100320; Biolegend) and anti-CD8-FITC (#100706; Biolegend) in PBS for 30 min at 4 °C. Intracellular staining of GzmB was performed as follows: cells were washed and then fixed and permeabilized with a Fix/Perm kit (#421403; Biolegend) and finally stained with anti-APC-GzmB (#372204; Biolegend). For proper compensation of flow cytometry channels, single-stain samples were utilized. The stained cells were analyzed on the flow cytometer (Beckman Coulter Cytoflex), and data were analyzed using CytExpert2.4 software.
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