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8 protocols using lsr 2

1

Flow Cytometry Cell Purity Assay

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Primary cells were stained for purity post-isolation using anti-CD45 (HI30, BD), anti-CD8 (RPA-T8, BD), and Near IR Live/dead stain (Invitrogen), then fixed with 4% formaldehyde (Thermo) and analyzed using a BD LSR II or a Cytek Aurora cytometer. Data were analyzed using FlowJo 10 software.
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2

Multiparametric Flow Cytometry of Murine Liver Cells

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Single cell suspensions of livers were washed in PBS prior to viability staining (Zombie Near-InfraRed) and staining for surface proteins for 30 minutes. Excess antibody was washed out with PBS prior to sample fixation. All antibodies were used at a 1:200 dilution, except F4/80-PE-Cy7 which was used at 1:150, for 30 minutes on ice. Samples were analyzed using a BD LSR-II (4 lasers) and a Cytek Aurora (4 lasers). Antibodies used for flow cytometry included the following: BV421 anti-mouse F4/80 (BD, 100433), eFluor 506 anti-mouse CD45 (Invitrogen, 69-0451-82), FITC anti-mouse Ly6G (BD, 553127), PerCP/Cyanine5.5 anti-mouse CD4 (Biolegend, 12-0114-81), PE anti-mouse CD11c (Invitrogen, 25-0032-82), PE Cyanine 7 anti-mouse CD3 (Invitrogen, 565411), APC anti-mouse CD11b (Biolegend, 101211) and live/dead near-IR dead cell stain kit (Invitrogen, L34975).
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3

Tumor Immune Cell Isolation and Analysis

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Mice were sacrificed, TDLN, spleen and tumors were removed. We placed the spleens and lymph nodes between the frosted surfaces of two glass slides and applied force to disrupt these organs to release immune cells, spleen was need to treated with ACK lysis buffer to remove red blood cells. Single-cell suspensions were filtered through a 40-μm cell strainer, washed, and resuspended in 1%FBS HBS for analysis. Tumor were cut into small pieces, digested in serum free RPMI with 0.25 mg/ml Liberase TL (Roche) and 0.33 mg/ml Dnase 1 (Sigma) in 37° for 30 min. Single-cell suspensions were filtered through a 40-μm cell strainer, washed, and resuspended in 1%FBS HBS for staining. For IFN-γ or Granzyme B staining, tumor cells were stimulated with leukocyte activation cocktail (Biolegend) for 6 h, then stained surface marker and intracellular markers. by the standard staining protocol described before (Chen et al., 2020 (link)). Flow cytometry analysis were applied to LSRII or Aurora (Cytek Biosciences) and analyzed by using Flowjo software (BD).
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4

Flow Cytometry Cell Purity Assay

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Primary cells were stained for purity post-isolation using anti-CD45 (HI30, BD), anti-CD8 (RPA-T8, BD), and Near IR Live/dead stain (Invitrogen), then fixed with 4% formaldehyde (Thermo) and analyzed using a BD LSR II or a Cytek Aurora cytometer. Data were analyzed using FlowJo 10 software.
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5

Analyzing Flow Cytometry Data for EBV Response

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Flow cytometry data were acquired on an LSR-II (for conventional flow cytometry) and Cytek Aurora (for full spectrum flow cytometry) and analysed using FlowJo software version 10.8.1. Statistical analysis was performed using STATA version 13 (StataCorp, College Station, Texas USA) and GraphPad Prism version 8.0.1 for graphical representation. Both nonparametric tests including Mann-Whitney and Kruskal Wallis, Spearman’s rank correlation as well as parametric tests including one-way ANOVA and student T-test were used for statistical analysis of quantitative data appropriately. False Discovery Rate (FDR) was used to adjust for multiple comparisons. Logistic regression analysis adjusting for testing batch and sex as well as the chi2 test were used to analyse qualitative IFN-γ responses to EBV by age groups.
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6

Lymphocyte Phenotyping by Flow Cytometry

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Single cell suspensions were prepared from indicated organs and indicated fluorophore-conjugated antibodies (Biolegend, Tonbo, eBioscience) used to stain lymphocytes. Flow cytometry was performed on a BD Biosciences LSR II or Cytek Biosciences Aurora, and data were analyzed with FlowJo software.
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7

Multiparametric Flow Cytometry of Lymphocytes

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Lymphocytes isolated from spleen, blood, and lymph nodes were stained with H-2Db/GP33 (MHC class I tetramer) or congenic markers (CD45.1/CD45.2), together with antibodies against cell surface antigens for 30–60 min at 4°C. For Granzyme B and cytokine staining, cells were then fixed with the paraformaldehyde Fixation Buffer (Biolegend) for 20 min at RT. For transcription factor staining, cells were fixed with True-Nuclear Transcription Factor Buffer Set (Biolegend) overnight at 4°C. Intracellular and transcription factor stains were performed in Intracellular Staining Permeabilization Wash Buffer (Biolegend). Flow cytometry data were acquired on an LSRII, FACSCelesta or Cytek Aurora flow cytometer and analyzed using FlowJo or Cytobank.
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8

Multiparametric Flow Cytometry of Lymphocytes

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Lymphocytes isolated from spleen, blood, and lymph nodes were stained with H-2Db/GP33 (MHC class I tetramer) or congenic markers (CD45.1/CD45.2), together with antibodies against cell surface antigens for 30–60 min at 4°C. For Granzyme B and cytokine staining, cells were then fixed with the paraformaldehyde Fixation Buffer (Biolegend) for 20 min at RT. For transcription factor staining, cells were fixed with True-Nuclear Transcription Factor Buffer Set (Biolegend) overnight at 4°C. Intracellular and transcription factor stains were performed in Intracellular Staining Permeabilization Wash Buffer (Biolegend). Flow cytometry data were acquired on an LSRII, FACSCelesta or Cytek Aurora flow cytometer and analyzed using FlowJo or Cytobank.
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