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105 protocols using 7 aad viability staining solution

1

Evaluating Apoptosis in Hematopoietic Stem Cells

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Cell apoptosis was evaluated using Pacific Blue Annexin V (Biolegend, 640918) and 7-AAD Viability Staining Solution (BioLegend, 420403). In detail, GE-HSPCs were stained with the following antibodies mix for 15 min at 4°C: CD34 PE (Miltenyi Biotec 130-081-00), CD90 APC (BD Biosciences, 559869), and CD133/1 PECy7 (Miltenyi Biotec, 130-101-652). Cells were then washed with diluted 1:10 10X Annexin V Binding Buffer (BD Pharmingen, 556454) upon surface marker staining and stained with Pacific Blue Annexin V (Biolegend, 640918) and 7-AAD Viability Staining Solution (BioLegend, 420403) for 15 min at RT in the dark. After staining, cells were washed in 1X Annexin V Binding Buffer and acquired in 10 min. All samples were run on BD FACSCanto II cytometer (BD Biosciences). At least 10,000 were recorded. Analysis of flow cytometry results was performed using FlowJo software.
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2

Apoptosis and Lipid Peroxidation Assay

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For 7-AAD and annexin V staining, cells were harvested and the pellets were washed twice with cold cell staining buffer (2% FBS in PBS). 1 × 106 cells were resuspended in 100 μl Annexin V Binding Buffer with 5 μl APC Annexin V and 5 μl 7-AAD Viability Staining Solution (BioLegend, 640930). Cells were gently vortexed and then incubated at room temperature (25 °C) in the dark for 15 min. 400 μl of Annexin V Binding Buffer was added to each tube before flow cytometry analysis. For lipid peroxidation measurement, cells were incubated in the culture medium containing 2 μM BODIPY 581/591 C11 (Lipid Peroxidation Sensor) (ThermoFisher, D3861) at 37 °C for 30 min. After staining, cells were washed and resuspended in fresh Cell Staining Buffer (2% FBS in PBS). Cells were processed on an Invitrogen Attune NxT Acoustic Focusing Cytometer and analyzed by FlowJo software. A representative gating strategy for flow cytometry analysis is shown in Supplementary Fig. 11.
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Comprehensive Phenotyping of Tumor-Infiltrating Lymphocytes

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Cell viability was assessed by live labeling 0.1 × 106 TILs with 7-AAD viability staining solution (Biolegend) (22 (link)). For purity, cells were stained with FITC anti-CD3 and PerCP anti-CD19 antibodies. For phenotyping, approximately 0.5 × 106 TILs were stained for measuring the percentages of Treg and TEM cells using standard flow cytometry staining protocols (22 (link)). Briefly, for Treg cells, TILs were labelled live with the following antibodies: FITC anti-CD3, PE anti-CD127, PerCP anti-CD8, APC anti- CD4, APC-Cy7 anti-CD25 and PB anti-CD45. For TEM cells, TILs were labeled live with the following antibodies: FITC anti-CD45, PE anti-CD4, PerCP anti-CD8, PE-Cy7 anti-CCR7, APC anti-CD45RO, APC-Cy7 anti-CD3 and PB anti-CD45RA (all flow cytometry antibodies from BD Biosciences). Samples were fixed in 1% paraformaldehyde solution, read on a BD FACSCanto flow cytometer (BD Biosciences, San Jose, CA) and analyzed by FCS Express software (DeNovo Software,).
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Cytotoxicity Assay of PD-L1-specific HTLs

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Cytotoxic activity of CD4+ HTL lines was measured by flow cytometry using the BD Accuri C6 flow cytometer and software (BD Biosciences). HSC-4, Lu65 (matched HLA-DR with PD-L1-specific HTLs), and SAS (unmatched HLA-DR with PD-L1-specific HTLs) were labeled by using the CellTrace™ CFSE Cell Proliferation Kit (Life Technologies) after pretreatment with or without IFN-γ (500 U/ml) for 24 h. After co-culture with PD-L1-specific HTLs for 6 h, tumor cells were collected, and dead cells were detected with 7-AAD viability staining solution (BioLegend). Cytotoxicity of PD-L1-specific HTLs was assessed in various effector/target cell (E:T) ratios (0:1, 10:1, and 30:1).
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5

Flow Cytometry Immunophenotyping Protocol

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1 × 105 cells were used for each staining, including a non-stained sample for each set of measurements. Briefly, cells were washed twice in PBS (Sigma-Aldrich, Munich, Germany) and incubated for 10 min at 4 °C in 40 μL blocking buffer, composed of 39 μL 1% Bovine Serum Albumin (BSA) (Sigma-Aldrich, Munich, Germany) in PBS (Sigma-Aldrich, Munich, Germany) and 1 μL FcR human blocking reagent (Miltenyi, Bergisch Gladbach, Germany). Cells were then incubated with conjugated antibodies (PE anti-human CD235a (Glycophorin A) Antibody (clone HIR2), FITC anti-human CD71 Antibody (clone CY1G4), FITC anti-mouse/human CD44 Antibody (clone IM7), FITC anti-human CD49d Antibody (clone 9F10), all from Biolegend, San Diego, CA, USA, and at concentrations suggested by the manufacturer) for 30 min at 4 °C in the dark and analyzed using a CyFlow Cube 8 6-channel instrument (Sysmex Partec, Münster, Germany). For cell death assessment, cells were incubated for 10 min at 4 °C in the dark with 7-AAD Viability Staining Solution (Biolegend, San Diego, CA, USA) according to the manufacturer’s instructions. A minimum of 0.5 × 105 cellular events was recorded and data were analyzed and visualized using FCS Express 4 (DeNovo Software).
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PMA, Ionomycin, and BFA Stimulation Protocol

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Phorbol 12-myristate 13-acetate (PMA), ionomycin, and Brefeldin A (BFA) were obtained from Multisciences (China). Recombinant human IL-21 (rhIL-21) was purchased from PeoproTech GmbH (Rocky Hill, CT, USA). Anti-GrB antibody and isotype control were purchased from R&D Systems (Minneapolis, MN, USA). CpG ODN 2006 was purchased from InvivoGen (San Diego, CA, USA). Anti-human IgM + IgG for B-cell receptor (BCR) stimulation and APC-Cyanine7-anti-human CD19 antibody, FITC-anti-human CD4 antibody, PerCP-Cyanine5.5-anti-human CD4 antibody, FITC-anti-human CD14 antibody, PE-anti-human-IL-21 receptor (IL-21R) antibody, PE-Cyanine7-anti-human CD25 antibody, PE-anti-human GrB antibody, FITC-anti-human IFN-gamma antibody, and eFluor® 660-anti-human IL-17A antibody for immunostaining were purchased from eBioscience (San Diego, CA, USA). Alexa Fluor® 700-anti-human CD3 antibody, Brilliant Violet 570-anti-human CD56 antibody, APC-annexin V, and 7-AAD viability staining solution were purchased from Biolegend (San Diego, CA, USA).
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7

Multicolor flow cytometry of murine tumors

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Fluorophore conjugated antibodies specific for human HLA-A, B, C (W6/32, 311403), mouse CD45.2 (104, 109814), mouse H-2Kb (AF6–88.5, 116518), mouse PD-L1 (10F,9G2, 124312), mouse OVA-Kb (25-D1.16, 141603), and 7-AAD Viability Staining Solution (420403) from BioLegend were used in flow cytometry. Rat anti-mouse CD16/CD32 (2.4G2, 553142) was purchased from BD Biosciences. Mouse tumors were dissociated to single cell suspension with Tumor Dissociation Kit (130-096-730) and gentleMACS Dissociator (130-093-235) from Miltenyi Biotec. All flow cytometry analyses were performed on a MACSQuant analyzer 10 (Miltenyi) and interpreted using FlowJo10 (Treestar).
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8

Adoptive Transfer of CD4+ and Th17 T Cells

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For the adoptive transfer of CD4+ T cells, mice were either treated with DSS or regular drinking water. On day 7 after DSS treatment, colons and mesenteric lymph nodes were removed and processed into single-cell suspensions as described above. Then, CD4+ T cells were isolated using a negative selection CD4+ T cell isolation kit from Miltenyi Biotec (Cat# 130–104-454). The purity of the cells isolated was checked by flow cytometry. 1×106 cells were transferred i.p. into naïve recipients on the day before infection with C. difficile.For the adoptive transfer of Th17 cells, splenocytes were isolated from IL17A-GFP reporter mice and cultured ex vivo using a CellXVivo Mouse Th17 Cell Differentiation Kit (R&D Systems, Cat# CDK017) according to the manufacturer’s instructions. After differentiation, the cells were stained for CD3e and CD4 expression and viability was determined using 7-AAD Viability Staining Solution (BioLegend, Cat# 420404). IL-17A+ and IL-17A- CD4+ T cells were sorted using an Influx Cell Sorter (BD Biosciences) and 1×106 cells were transferred into naïve recipients on the day before C. difficile infection.
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9

Cell Surface Marker Analysis by FACS

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Cells were washed with cold fluorescence-activated cell sorting (FACS) buffer (phosphate-buffered saline (PBS) containing 1% sodium azide and 2% FBS) and incubated with the indicated mAbs at 4 °C for 30 min, after blocking with purified mouse IgG (BioLegend, clone MG1-45, 0.5 μg/mL, 4 °C, 15 min). After several washes, the cells were stained with 7-AAD Viability Staining Solution (BioLegend) and analyzed using a BD FACSAria III Cell Sorter (BD, Franklin Lakes, NJ, USA) and FlowJo software version 10 (BD).
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10

Evaluating CAR-T Cell Cytotoxicity Against VEGFR2+ Targets

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EL4 cells that do not express VEGFR2 were labeled with Tag-It Violet Proliferation Cell Tracking Dye (Biolegend), and VEGFR2+ EL4 cells were labeled with Cell Proliferation Dye eFluor 670 (Thermo Fisher Scientific). Mouse CAR-T cells 4 days after Rv transduction, EL4 cells, and VEGFR2+ EL4 cells were co-cultured at the indicated E/T ratios. After 18 h, CountBright Absolute Cell Counting Beads (Thermo Fisher Scientific) and 7-AAD Viability Staining Solution (Biolegend) were added to the reaction wells, and the number of each target cell was analyzed using flow cytometry until 1000 beads were detected. Cytotoxicity was calculated using the following formula: Percentage of antigen-specific lysis = [(VEGFR2+ EL4 cells/ EL4 cells ratio in non-effector cell’s well) − (VEGFR2+ EL4 cells/ EL4 cells ratio in effector cell’s well)] / [VEGFR2+ EL4 cells / VEGFR2 EL4 cells ratio in non-effector cell’s well] × 100.
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