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22 protocols using foxp3 fix perm buffer

1

Peripheral Blood Mononuclear Cell Immunophenotyping

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Surface Staining: Harvested PBMCs were stained with fixable Live/Dead stain (Invitrogen) in PBS for 30 min on ice. Cells were washed and stained with surface markers in FACS buffer (PBS/1%BSA /2mM EDTA) for 30 min on ice.
Fixation and staining of intracellular markers: For the effector panel, cells were washed prior to fixation in 4% PFA for 5 min, 37 C. Cells were washed in FACS buffer, and resuspended in permeabilization buffer (eBioscience, San Diego, CA) for 20 mins at room temperature. Antibodies against intracellular targets were added and cells were incubated for 45 mins, on ice. For the regulatory panel, cells were washed with FACS buffer, and fixed with Foxp3 Fix/Perm buffer (eBioscience, San Diego, CA) for 30 mins, on ice. After washing in permeabilization buffer, cells were stained with antibodies detecting intracellular markers in permeabilization buffer for 45 mins, on ice.
Stained and permeabilized cells were washed twice in permeabilization buffer before resuspension in FACS buffer, and subsequently acquired on an LSR Fortessa (BD Biosciences). Antibodies used for the regulatory panel are shown in Table 2.
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2

Comprehensive Immune Cell Profiling

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Surface staining of the single cell suspensions was performed for 30 min at 4°C, and viability was assessed using LIVE/DEAD Fixable viability dye as per the manufacturer’s instructions (Thermo Fisher Scientific).
The following surface markers antibodies from Biolegend were used: anti-CD3 (clone: 145–2C11), anti-CD4 (RM4–5), anti-CD8a (53–5.8), anti-CD45 (30-F11), anti-CD11b (M1/70), anti-CD11c (N418), anti-CD19 (6D5), anti-TCRβ (H57–597), anti-NK1.1 (PK136), anti-KLRG1 (2F1), anti-PD-1 (29F.1A12), anti-CD25 (PC-61), anti-CD44 (IM7), anti-CD62L (MEL-14), anti-Thy1.1 (OX-7), anti-CCR2 (SA203G11), anti-CXCR3 (CXCR3–173), anti-CXCR5 (L138D7), anti-CXCR6 (SA051D1), anti-CD103 (2E7). Samples were then fixed overnight at 4°C using the using 100 μL of Foxp3 Fix/Perm buffer (eBioscience). After membrane permeabilization using 1X permeabilization buffer (eBioscience) for 5 min, intracellular staining was performed for 120 min at room temperature using the following antibodies: anti-Ctla-4 (UC10–4B9, Biolegend), anti-Helios (22F6, Biolegend), anti-Foxp3 (FJK16, Thermofisher), anti-Gata3 (TWAJ, Thermofisher), anti-RORγ (AFKJS-9, Thermofisher), anti-Ki-67 (16A8, Biolegend). Cells were acquired with an Aurora flow cytometer (Cytek Biosciences) or a FACSymphony flow cytometer (BD Biosciences). Data were analyzed using FlowJo software version 10 (TreeStar, BD LifeSciences).
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3

Single-cell analysis of lung cells

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Lungs were minced and enzymatically digested using collagenase D (from Clostridium histolyticum; Roche) for 1 h at 37°C (for virus-infected lungs) or incubated at 37 C for 30 min in HBSS containing collagenase type 4 (8480 U/mL), elastase (7.5 mg/mL), and soybean trypsin inhibitor (2 mg/mL) (all from Worthington Industries) (for tumor-containing lungs). Lungs were then mechanically disrupted to single-cell suspensions, subjected to red blood cell lysis, washed and resuspended for staining. Cell suspensions were stained with cisplatin (Fluidigm), incubated with Fc receptor blocking antibody (2.4G2, Tonbo Biosciences) for 20 minutes, following by addition of primary surface antibodies incubated for 15 minutes at 37 C and 15 minutes at 22 C. Secondary surface stains were done for 20 minutes, with intracellular antigen staining done using the eBioscience FoxP3 Fix/Perm buffer and 2 hour stain at 4 C. Following cell staining, cells were washed and resuspended in Intercalator (Cell-ID™ Intercalator-Ir, Fluidigm). Antibodies are indicated in Supplemental Table 1 and 2 and were from Fluidigm unless noted otherwise.
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4

Intracellular Flow Cytometry of Thymocytes

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Cytoplasmic and nuclear proteins were examined via intracellular flow cytometry. Thymocytes were labelled with surface markers for iNKT cells before being fixed and permeablized with Foxp3 fix:perm buffer (eBioscience) or cytofix/cytoperm (BD), according to their respective intracellular staining protocols.
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5

Multiparametric Phenotyping of Mouse Cells

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The following directly labeled anti-mouse monoclonal antibodies were used for BM cell phenotypical analysis: CD90.2-APC and CD45-PE/Cy7 for lymphoid progenitors, CD61-APC and CD41-FITC for megakaryocytic population, CD71-PE and Ter119-FITC for erythroid precursors, CD11b-PE and Gr1-FITC for granulocytes/monocytes progenitors, Lineage Cocktail (CD3, Gr1, CD11b, CD45R, Ter119)-FITC, Sca1-PE, cKit (CD117)-APC for hematopoietic stem cells, all purchased from BioLegend (BioLegend, San Diego, CA, USA).
The phenotypical analysis of splenocytes was performed using the following anti-mouse antibodies: CD4-PE/Cy5, CD8a-PE (BioLegend) for helper and cytotoxic T cells, CD19 (BioLegend) for B cells, CD11c-PE, I-Ab-FITC, and TLR4 (CD284)-PE/Cy7 (all from BioLegend) for dendritic cells (DCs), and NK1.1-FITC (BioLegend) for NK cells. To detect proliferative cells, Ki67-eFluor660 (eBioscience, San Diego. USA) was used.
Single-cell suspensions of splenocytes or BM cells were incubated with the fluorescently labeled antibodies in PBS containing 1% BSA, at 4°C for 20 min for cell surface staining. For intracellular staining (Ki67), cells were permeabilized using the Foxp3 Fix/Perm Buffer (eBioscience), according to the manufacturer’s instructions. Measurements were performed with a FACSCalibur flow cytometer as described above.
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6

Multiparameter Immunophenotyping Protocol

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The following antibodies were used for surface staining at 4°C for 30 min: anti-CD4 (Biolegend, RM4-5), anti-ICOS (Biolegend, 15F9), anti-CD19 (Biolegend, 6D5), anti-PD-1 (Biolegend, RMP1-30), anti-CXCR5 biotin (BD Biosciences, 2G8), T- and B-cell activation antigen (BD Biosciences, GL-7), CD38 (Biolegend, 90), CD138 (Biolegend, 281-2), and anti-CD95 (BD Biosciences, Jo2), Streptavidin-BV421 (Biolegend, 405225). For intracellular staining, samples were fixed with the Foxp3 Fix/Perm buffer set according to the manufacturers instructions (eBioscience). Samples were then intracellularly stained with anti-FoxP3 (eBiosciences, FJK-16S). No viability dye was included. Samples were analyzed on FACS Canto II (BD) or Cytek Aurora. Data was analyzed using FlowJo v10 (FlowJo LLC).
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7

Multi-parameter Flow Cytometry Analysis

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Labeled and purified antibodies were purchased from BD Biosciences, BioLegend, or eBioscience (Table 1). Single cell suspensions were incubated sequentially with anti-CD16/32 (to block Fc receptors) then primary antibodies. Data were collected on a Gallios flow cytometer (Beckman Coulter) and analyzed using FlowJo software (Tree Star). For intracellular cytokine analysis, 5–10 × 105 leukocytes were restimulated with ionomycin (1 µg/ml) and PMA (25 ng/ml) in the presence of Brefeldin A (10 µg/ml) for 4.5–5 h at 37°C. Following staining for surface antigens, cells were stained for intracellular cytokines using a Cytofix/Cytoperm kit (BD Bioscience), according to the manufacturer’s instructions. For short-term pulse BrdU labeling, mice were injected intraperitoneally with 1 mg/mouse BrdU (Sigma-Aldrich) in 100 µl PBS 1 h before sacrifice. BrdU incorporation was examined using a BrdU flow kit (BD Biosciences), according to the manufacturer’s instructions. For the intracellular staining of Foxp3 and Ki-67, 1 × 106 leukocytes were stained for surface antigens and then were fixed and permeabilized with Foxp3 Fix/Perm Buffer (eBioscience) according to the manufacturer’s instructions.
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8

Multiparameter Flow Cytometry Analysis

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The following antibodies were used for surface staining: anti-CD4 (RM4-5), anti-ICOS (15F9), anti-CD19 (6D5), anti-CD25 (PC61), anti-CXCR5 biotin (2G8), GL7 (GL-7), anti-PD-1 (RMP1-30), anti-GITR (DTA-1), anti-Thy1.1 (OX-7), anti-CD45.1 (A20), and anti-IA (M5/114.15.2). For intracellular staining, samples were fixed with the FoxP3 Fix/Perm buffer set according to the manufacturer’s instructions (eBioscience). Samples were then intracellularly stained with anti-IgG1 (A85-1), anti-FoxP3 (FJK-16S), anti-Ki67 (B56), anti-Glut1 (polyclonal; Abcam), anti-Helios (22F6), or CTLA-4 (UC10-4B9).
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9

Multiparametric Flow Cytometry Analysis

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The following antibodies were used for surface staining: anti-CD4 (RM4-5), anti-ICOS (15F9), anti-CD19 (6D5), anti-CXCR5 biotin (2G8) and GL7 (GL-7). For intracellular staining, samples were fixed with the FoxP3 Fix/Perm buffer set according to manufacturer’s instructions (eBioscience). Samples were then intracellularly stained with IFN-γ (XMG1.2), IL-17A (TC11-18H10.1), anti-IgG1 (A85-1), anti-FoxP3 (FJK-16S), and Ki-67 (B56). Antibodies were from BioLegend, BD Biosciences, or eBioscience. Flow cytometry data were acquired on a FACSCalibur (BD) or LSRII (BD) using FACSDiva software (BD), and analyzed with FlowJo software (FlowJo LLC).
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10

Lymph Node Immune Cell Profiling

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Axillary and inguinal lymph nodes or deep cervical lymph nodes were isolated and mashed through a 70 μm strainer in PBS containing 1% BSA and 2 mM EDTA. The following antibodies were used, and are all from eBioscience unless otherwise noted: Foxp3-Alexa 488, CD4-PerCp Cy5.5, TCRβ-APC eFluor780, CD45-APC, CD8-eFluor 450, CD25-PE (BD Bioscience), IL-4-PE, IFN-γ-APC, and CD69-PE Cy7. For intranuclear staining, the cells were fixed overnight in Foxp3 Fix/Perm buffer (eBioscience) before incubating with Foxp3 antibody in FACS buffer containing 0.3% saponin (Fisher). For intracellular staining, mice were injected with 3 μg of BrefeldinA 5 hours before they were sacrificed. The cells were stained for extracellular markers before they were fixed in IC Fixation buffer (eBioscience) for 30 minutes, then permeabilized and stained for intracellular antigens in FACS buffer containing 0.3% saponin.
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