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10 protocols using anti cd45.1 a20

1

Cytofluorimetry Gating and Proliferation

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For cytofluorimetry, gating was performed on viable cells based on forward scatter and side scatter profiles. Fluorescently labeled antibodies were purchased from eBioscience (anti-CD45.1, A20; anti-CD4, RM4–5; anti-CD11c, N418) or BioLegend (anti-CD45.2, 104; anti–I-A/I-E, M5/114.15.2). Proliferation was assessed using the dye CellTrace Violet (Life Technologies) according to manufacturer’s instructions. Staining for cell surface markers was performed at 4°C for 30 m. Flow cytometry data were acquired on an LSRFortessa (Becton Dickinson) instrument and analyzed with the FlowJo software package (Tri-Star).
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2

Immunophenotyping of Murine Splenocytes and Thymocytes

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Mouse splenocytes and thymocytes were prepared from pooled thymus or spleen. Thymic and splenic cells were pre-incubated with Fc-block before staining with other antibodies. The mouse antibodies used included anti-CD4 (RM4–5, eBioscience); anti-CD8 (53–6.7, eBioscience); anti-CD45.1 (A20, BioLegend), anti-CD45.2 (104, eBioscience); anti-CD25 (PC61.5, eBioscience); anti-CD69 (H1.2F3, eBioscience); anti-CD24 (M1/69, eBioscience); anti-Helios (22F6, eBioscience) before flow cytometry analysis. For intracellular staining of Ki-67 (B56, BD), pSTAT5 (47/Stat5(pY694), BD) and Foxp3 (NRRF-30, eBioscience), cells were fixed and permeabilized with BD Cytofix/Cytoperm™ Fixation / Permeabilization Solution Kit (554,714, BD) and stained according to the manufacturer’s protocols. The CD4+ T cells from the thymus and spleen of WT or RelB−/− mice were analyzed by flow cytometry and gated as shown in the Supplementary Figure 1. The samples were analyzed using a BD LSRFortessa flow cytometer and FlowJo software (Tree Star Inc). All single-cell suspensions from the tissues were stained with Abs diluted in PBS containing 2% FCS for 30 min on ice.
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3

Multicolor Flow Cytometry Staining

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Anti-CD11c (N418), anti-F4/80 (BM8), anti-CD19 (6D5), anti-CD11b (M1/70), and anti-CD45.1 (A20) were from BioLegend. Anti-ST2 (U29-93), anti-CD3 (17A2), anti-CD4 (RM4-5), anti-IFNγ (XMG1.2), and anti-CD16/32 (2.4G2) were from BD Biosciences. CellTrace Violet, Fixable Viability Dye eFluor 780, and Foxp3 (FJK-16s) were from Thermo Fisher Scientific. Anti-4-1BB (158332) was from R&D.
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4

Characterization of CD8+ T Cell Phenotypes

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Single-cell suspensions were prepared from the spleen, LNs, and surface or intracellularly stained as described (Shan et al., 2022a (link)). The fluorochrome-conjugated antibodies were as follows: anti-CD8 (53–6.7), anti-TCRβ (H57-597), anti-CD45.2 (104), anti-Granzyme B (GB12), anti-IFN-γ (XMG1.2), anti-Tbet (4B10), anti-CD62L (MEL-14), anti-KLRG1 (2F1), anti-CD25 (PC61.5), anti-CD69 (H1.2F3), and anti-CD44 (IM7) were from Thermo Fisher Scientific; anti-Tcf1 (C63D9) from Cell Signaling Technology; anti-IL-7Rα (A7R34) and anti-CD45.1 (A20) were from BioLegend. For detection of Tcf1 and Tbet proteins, surface-stained cells were fixed and permeabilized with the Foxp3/Transcription Factor Staining Buffer Set (eBiosciences, Thermo Fisher Scientific), followed by incubation with corresponding fluorochrome-conjugated antibodies. Apoptotic cells were detected with FLICA 660 Caspase-3/7 detection kit (Bio-Rad). Data were collected on FACSCelesta or FACSVerse (BD Biosciences) and were analyzed with FlowJo software V10.2 (TreeStar). For validation of CTCF deletion efficiency, cell lysates from sorted GFP+ naive or early effector CD8+ T cells were immunoblotted with anti-CTCF antibody (D31H2; Cell Signaling Technology) following standard protocols.
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5

Multiparametric Flow Cytometry Profiling

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For cell surface staining, cells were pre-incubated with 2.4G2 Fcγ RII/RIII blocking mAb for 15 minutes and then stained with the appropriate combinations of mAbs diluted in HBSS + 2% FBS for 30 minutes at 4°C. Cells were analyzed on a BD FACS CantoII, or Cytek Aurora Spectral Cytometer and data were processed with FlowJo software (TreeStar). The complete list of antibodies use is as follows: anti-human Vβ5.1 (LC4, Invitrogen), anti-TCRβ (H57–597, BioLegend), anti-CD44 (IM7, BioLegend), anti-Vβ11 (KT11, BioLegend), anti-CD45.2 (104, BioLegend), anti-CD45.1 (A20, BioLegend), anti-SiglecF (E50–2440, BD Bioscience), anti-CD45 (30-F11, BioLegend), anti-CD11c (N418, BioLegend), anti-CD11b (M1/70, BioLegend), anti-Ly6G (1A8, BioLegend), anti-CD19 (6D5, BioLegend), anti-NK1.1 (PK136, BioLegend), anti-CD3 (17A2, BioLegend), Zombie Red (BioLegend), anti-mouse CD185/CXCR5 (L138D7, Biolegend), anti-mouse CD279/PD-1 (29F.1A12, Biolegend), and anti-Ki67 (SolA15, Invitrogen).
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6

Comprehensive Flow Cytometry and ChIP Analysis

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For flow cytometry analysis, the following antibodies were used at a 1:100 dilution: anti-CD3 (17A2; Biolegend), anti-CD4 (GK1.5; Biolegend), anti-CD25 (PC61; Biolegend), anti-CD44 (IM7; Biolegend), anti-CD62L (MEL-14; Biolegend), anti-CD45.1 (A20; Biolegend), anti-CD45.2 (104; Biolegend), anti-FasL (MFL3; Biolegend), anti-IL-17A (TC11-18H10.1; Biolegend), anti-IFN-γ (XMG1.2; Biolegend), anti-JunB (C-11; Santa Cruz Biotechnology, Santa Cruz, CA, USA), anti-GATA3 (16E10A23; Biolegend), anti-ROR-γt (Q31-378; BD), anti-T-bet (4B10; Biolegend), and anti-rabbit IgG (Poly4064; Biolegend). For ChIP analyses, anti-JunB (1 μg per ChIP, 210; Santa Cruz), anti-BATF (1 μg per ChIP, WW8; Santa Cruz), anti-IRF4 (1 μg per ChIP, M-17; Santa Cruz) and rabbit IgG (1 μg per ChIP, I5006; Sigma) were used.
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7

Monoclonal Antibodies for Hematopoietic Cell Analysis

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The following monoclonal antibodies (Abs) were used for flow cytometry and cell sorting: anti-c-Kit Microbeads (Miltenyi Biotec), anti-c-Kit (2B8, BD Biosciences / Biolegend), anti-Sca-1 (E13–161.7, BD Biosciences / Biolegend), anti-CD45.1 (A20, Biolegend), anti-CD45.2 (104, BD Biosciences), anti-CD4 (RM4–5, BD Biosciences), anti-B220 (RA3–6B2, BD Biosciences), anti-TER-119 (TER-119, Biolegend), anti-Gr-1 (RB6–8C5, BD Biosciences/Biolegend), anti-Mac-1 (M1/70, BD Biosciences), anti-CD71 (C2, BD Biosciences), anti-CD43 (S7, BD Biosciences), anti-CD16/32 (2.4G2, BD Biosciences), anti-Ki67 (B56, BD Biosciences), anti-CD34 (RAM34, eBioscience), anti-CD135 (A2F10, Biolegend), The primary Ab used for immunocytochemistry (ICC) was goat anti-Tfe3 (p-16; Santa Cruz Biotechnology). Anti-phospho mTor (Ser2448), anti-phospho Akt (Thr308), and anti-beta actin from Cell Signaling were used for western blotting.
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8

Comprehensive Immune Cell Profiling

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For cell surface staining, cells were pre-incubated with 2.4G2 Fcγ RII/RIII blocking mAb for 15 min and then stained with the appropriate combinations of mAbs diluted in HBSS + 2% FBS for 30 min at 4 °C. Cells were analyzed on a BD FACS CantoII, or Cytek Aurora Spectral Cytometer, and data were processed with FlowJo software (TreeStar). The complete list of antibodies use is as follows: anti-human Vβ5.1 (LC4, Invitrogen), anti-TCRβ (H57-597, BioLegend), anti-CD44 (IM7, BioLegend), anti-Vβ11 (KT11, BioLegend), anti-CD45.2 (104, BioLegend), anti-CD45.1 (A20, BioLegend), anti-SiglecF (E50-2440, BD Bioscience), anti-CD45 (30-F11, BioLegend), anti-CD11c (N418, BioLegend), anti-CD11b (M1/70, BioLegend), anti-Ly6G (1A8, BioLegend), anti-CD19 (6D5, BioLegend), anti-NK1.1 (PK136, BioLegend), anti-CD3 (17A2, BioLegend), Zombie Red (BioLegend), anti-mouse CD185/CXCR5 (L138D7, Biolegend), anti-mouse CD279/PD-1 (29 F.1A12, Biolegend), and anti-Ki67 (SolA15, Invitrogen).
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9

Detailed Antibody Staining for Hematopoietic Cells

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The following antibodies (all from eBioscience, unless otherwise stated) were used: BM cell populations: anti-CD11b (M1/70) and anti-Gr1 (RB6-8C5). Assessment reciprocal BM chimeric mice: anti-CD45.1 (A20, BioLegend) and anti-CD45.2 (104). Hematopoietic stem and progenitor cells (HSPCs): anti-CD3ɛ (145-2C11), anti-CD4 (GK1.5, BioLegend), anti-CD8α (53-6.7, BioLegend), anti-B220 (RA3-6B2), anti-CD11b (M1/70), anti-Gr1 (RB6-8C5), anti-Ter119 (TER-119, BioLegend), anti-IL7Rα (A7R34), anti-NK1.1 (PK136, BioLegend), anti-cKit (2B8), anti–Sca-1 (D7, BioLegend), anti-CD34 (RAM34), anti-FcγR (93), anti-CD48 (HM48-1), and anti-CD150 (TC15-12F12.2, BioLegend). Classical and plasmacytoid dendritic cells: anti-CD3e (145-2C11), anti-CD19 (MB19-1), anti-NK1.1 (PK136; Becton Dickinson), anti-CD45RA (14.8; BD Biosciences), anti-CD11c (N418), and anti-MHCII (M5/114.15.2). BM non-hematopoietic BM stromal cells: anti-Sca1 (D7, BioLegend), anti-Ter119 (TER-119, BioLegend), anti-CD45 (30-F11, BioLegend), anti-CD31 (390), anti-CD105 (MJ7/18), and anti-CD140b (APB5). Interleukin-6 (IL-6) receptor α and β subunits: anti-CD126 (D7715A7, BioLegend) and anti-CD130 (KGP130).
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10

Spleen Immunophenotyping After Infection

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Spleens from infected mice were harvested 7 d after infection and processed as described previously 66 . Sections were stained with anti-CD3 (17A2), anti-CD45.R/B220 (RA3-6B2) and anti-CD45.1 (A20; BioLegend). Spleen compartments were visualized by setting the density threshold of areas rich in CD3 (T cell zone) and B220 (B cell zone).
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