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10 protocols using igd 11 26c 2a

1

Multiparametric Flow Cytometry of Immune Cells

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BM, splenocytes, and LN cells were stained with fluorescent conjugated Abs specific for CD4 (GK1.5, Tonbo Biosciences), CXCR5 (L138D7, BioLegend), PD1 (29F.1A12, BioLegend), CD38 (90, BioLegend), GL7 (GL7, BioLegend), B220 (RA3-6B2, BioLegend), CD93 (AA4.1, BioLegend), CD19 (1D3, Tonbo Biosciences), CD21 (7E9, BioLegend), CD23 (BEB4, BioLegend), CD24 (M1/69, BioLegend), CD62L (MEL-14, Tonbo Biosciences), CD25 (7D4, Tonbo Biosciences), CD43 (S7, BD Pharmigen), IgD (11-26C.2A, BioLegend), and IgM (DS-1, BD Pharmigen); Igκ (1050-02; Southern Biotech); T-bet (EBIO4B10, eBiosciences) and Bcl6 (K112-91, eBioscience); and BrdU (BU20A, BioLegend). Other reagents include Caspase3/7 (C10427, Invitrogen), ghost dye (13-0865-T100, Tonbo Biosciences), and NP-PE (N-5070-1; Biosearch Technologies). Cells were analyzed by flow cytometry as previously described (86 (link)). VLP Ab was a gift from Shaun Jackson. Intracellular Bcl6 staining to identify Tfh cells was performed as previously described (87 (link)). Intracellular staining for T-bet was performed as previously described (23 (link)).
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2

Single-cell Immunophenotyping and Glucose Uptake

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Single-cell suspensions were prepared and stained as previously described (Lin et al., 2016 (link)). Antibodies used include rabbit anti-myc tag (71D10, Cell Signaling Technology), mouse anti-myc tag (4A6, Millipore), TCF1 (C63D9, Cell Signaling Technology), Pax5 (1H9, eBioscience), IgM (Il/41, eBioscience), IgD (11-26c.2a, BioLegend), CD23 (B3B4, eBioscience), CD4 (RM405, BioLegend), CD8α (53-6.7, eBioscience), and Gr1 (RB6-8C5, BD PharMingen). Glucose uptake was determined by staining with the fluorescent glucose analog 2-NBDG (Cayman, 100 μM) in glucose-free RPMI.
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3

Multiparametric Analysis of Immune Cells

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Cell suspensions prepared as described above were blocked with CD16/CD32 (Mouse BD Fc Block, 2.4G2, BD Biosciences). For B cell compartment analysis, suspensions were stained with antibodies against CD45 (30-F11, Tonbo), CD4 (GK1.5, eBioscience), CD19 (6D5, Biolegend), IgD (11–26c.2a, Biolegend), IgG (polyclonal, Jackson ImmunoResearch), IgM (II/41, Thermofisher), CD95 (DX2, Biolegend), and GL7 antigen (GL7, Biolegend). Dead cells were excluded with eBioscience Fixable Viability Dye eFluor 455UV (Thermofisher). In phagocyte depletion experiments, suspensions were stained with antibodies against CD45 (30-F11, Tonbo), I-A/I-E a (M5/114.15.2, Biolegend), CD11c (N418, Biolegend), CD11b (M1/70, Thermofisher), CX3CR1 (SA011F11, Biolegend), and CD103 (2E7, Thermofisher). Dead cells were excluded with eBioscience Fixable Viability Dye eFluor 506 (Thermofisher). Bacterial FISH staining was performed with Cy5-labeled EUB338 5’-GCTGCCTCCCGTAGGAGT-3’ probe (Integrated DNA Technologies; Table S1). Images were acquired under an inverted Nikon Eclipse Ti microscope (Nikon). Flow cytometry was performed using a LSRFortessa (BD Biosciences) and data were analyzed with FlowJo software (TreeStar).
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4

Single-cell Immunophenotyping and Glucose Uptake

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Single-cell suspensions were prepared and stained as previously described (Lin et al., 2016 (link)). Antibodies used include rabbit anti-myc tag (71D10, Cell Signaling Technology), mouse anti-myc tag (4A6, Millipore), TCF1 (C63D9, Cell Signaling Technology), Pax5 (1H9, eBioscience), IgM (Il/41, eBioscience), IgD (11-26c.2a, BioLegend), CD23 (B3B4, eBioscience), CD4 (RM405, BioLegend), CD8α (53-6.7, eBioscience), and Gr1 (RB6-8C5, BD PharMingen). Glucose uptake was determined by staining with the fluorescent glucose analog 2-NBDG (Cayman, 100 μM) in glucose-free RPMI.
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5

Spleen Tissue Cryosectioning and Immunofluorescence

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Spleen tissues were snap frozen in O.C.T. compound (4583; SAKURA) and stored at −80°C until frozen sectioning. The tissues were cut into 10 μm-thick cryosections and fixed with ice-cold acetone. The sections were rehydrated and blocked with 5% rat serum and 3% BSA with 0.1% Tween and stained with fluorescent-labeled antibodies and reagents, including CD4 (RM4-5; BioLegend), IgD (11-26c.2a; BioLegend), GL7 (GL7; BD Bioscience), and DAPI (R37606; Invitrogen). Images were obtained with an EVOS FL Imaging System (ThermoFisher).
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6

Comprehensive Murine Immune Cell Analysis

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Composition of murine immune cells was analyzed using the following antibodies: CD3 (145-2C11; BioLegend), CD19 (6D5; BioLegend), CD20 (SA275A11; BioLegend), CD11b (M1/70; BioLegend), CD11c (N418; BioLegend), CD45 (30-F11; BioLegend), Ly6C (HK1.4; BioLegend) and Ly6G (1A8: BioLegend). B cell maturation was analyzed using the following antibodies: CD19 (6D5; BioLegend), CD21 (7G6; BD Bioscience), CD23 (B3B4; BD Bioscience), CD93 (AA4.1; BioLegend), CD45R/B220 (RA3-6B2; BioLegend), IgD (11-26c.2a; BioLegend) and IgM (AF6-78; BD Bioscience). Monocyte, macrophage and microglia activation, differentiation and molecules involved in antigen presentation were determined using: CD40 (3/23; BD Bioscience), CD68 (FA-11; BioLegend), CD69 (H1.2F3; BioLegend), CD80 (16-10A1; BioLegend), CD86 (GL-1; BioLegend), MHCII (AF6-120.1; BioLegend) and PD-L1 (MIH5; eBioscience). Fc receptors were blocked using monoclonal antibody specific for CD16/ CD32 (93; BioLegend). Dead cells were stained with a fixable viability kit (BioLegend). Samples were acquired on a BD LSR Fortessa (BD Bioscience). All data evaluation was performed using FlowJo software (FlowJo LLC, Ashland, USA).
Intracellular proteins were analyzed using the BD PhosFlow protocol and analyzed using the following antibodies: BTK (53/BTK; BD Bioscience), pBTK (N35-86, BD Bioscience), iNOS (W16030C, Biolegend) Arg1 (A1exF5, eBioscience).
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7

Visualization of Germinal Center Structures

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Fresh tissues were snap-frozen in O.C.T. compound (Sakura Finetek USA) and stored at −80°C. Tissues were sectioned at 7 μm thickness (Leica). Prior to staining, sectioned tissues were fixed in cold acetone solution (Sigma) for 10 min then rehydrated with PBS for 10 min and blocked with 5% (w/v) bovine serum albumin (Sigma) and 2% (v/v) normal goat serum (NGS). Cell staining was performed using the following antibodies: IgD (11-26c.2a; Biolegend), B220 (RA3-6B2; BD), GL7 (GL7; Biolegend), CD35 (8C12; BD), CD3 (17A2; Biolegend), CD169 (3D6.112; BD), CD86 (GL1, Biolegend), CXCR4 (2B11; BD), CD4 (GK1.5; Biolegend), Ki67 (11F6, Biolegend), BCL6 (K112-91; BD). To amplify the CXCR4-PE signal, tissues were stained sequentially with rabbit anti-PE antibody (polyclonal; Novus Biologicals) and a secondary goat anti-rabbit IgG Alexa Fluor 555 antibody (polyclonal; Life Technologies). Slides were sealed with ProLong Diamond Antifade Mountant (Life Technologies). Tiled Z-stack images covering were captured on a Zeiss LSM710 microscope. Post-processing of confocal images was performed with ImageJ v2.0.0.
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8

Multiparametric Immunophenotyping of Immune Cells

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Human PBMC were stained for CD19 (HIB19; BioLegend), CD14 (M5E2; BD Bioscience) and MHC class II (G46-6; BD Bioscience). Composition of murine immune cells was analysed using the following antibodies: CD3 (145-2C11; BioLegend), CD19 (6D5; BioLegend), CD20 (SA275A11; BioLegend), CD11b (M1/70; BioLegend), CD11c (N418; BioLegend), CD45 (30-F11; BioLegend), Ly6C (HK1.4; BioLegend) and Ly6G (1A8: BioLegend). B cell maturation was analysed using the following antibodies: CD19 (6D5; BioLegend), CD21 (7G6; BD Bioscience), CD23 (B3B4; BD Bioscience), CD93 (AA4.1; BioLegend), CD45R/B220 (RA3-6B2; BioLegend), IgD (11-26c.2a; BioLegend) and IgM (AF6-78; BD Bioscience). Monocyte, macrophage and microglia activation, differentiation and molecules involved in antigen presentation were determined using: CD40 (3/23; BD Bioscience), CD68 (FA-11; BioLegend), CD69 (H1.2F3; BioLegend), CD80 (16-10A1; BioLegend), CD86 (GL-1; BioLegend), MHCII (AF6-120.1; BioLegend) and PD-L1 (MIH5; eBioscience). Fc receptors were blocked using monoclonal antibody specific for murine or human CD16/ CD32 (Murine TruStain FcX; Human TruStain FcX; BioLegend), respectively. Dead cells were stained with the Zombie Fixable Viability™ Kit (BioLegend). Samples were acquired on a BD LSR Fortessa (BD Bioscience). All data evaluation was performed using FlowJo software (FlowJo LLC, Ashland, USA).
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9

Isolation and Characterization of Murine Immune Cells

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Peyer’s patches and mLN were digested in digestion media (RPMI, 5% heat-inactivated FBS, 10 mM HEPES (pH 7.2), 1% pen/strep, 25mg/mL DNase I (Sigma,#DN25), and 0.5 mg/mL Collagenase IV (Worthington Biochemical,#LS004189) rotating at 37°C for 15 minutes. The digested tissue was then smashed through 70μm cell strainers. BM was harvested and cells were flushed with an insulin syringe and cells were filtered through a 70μm cell strainer. Single-cell suspension was then washed with FACS buffer (1X DPBS, 2% heat-inactivated FBS, 2mM EDTA) and counted for further analysis. Cells were incubated for 20 min on ice with antibodies to B220 (Clone RA3–6B2, Biolegend), IgG1 (RMG1–1,Biolegend), IgG2b (R12–3, Biolegend,IgA), IgG3 (R40–82, BDBioscience), GL7 (GL7, Biolegend), GL7 (GL7, Biolegend), CD138 (281–2, Biolegend), CD38 (90, Biolegend), CD45.2 (30-F11,ebioscience) (all used 1:500), IgA (polyclonal, Southern Biotech and IgD (11–26c.2a, Biolegend)(used 1:1000). Data were collected on a BD LSR II and analyzed in FlowJo v10.7 software.
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10

Confocal Imaging of Splenic Immune Cells

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Confocal imaging was performed on spleen sections. The following antibodies were used: IgM (II/41; Thermo Fischer Scientific), IgD (11-26.c2a; BioLegend), CD1d (1B1; eBioscience), CD169 (MOMA-1; Abcam). Briefly, 8-μm spleen frozen sections were fixed for 10 min in cold acetone. After washing with PBS, sections were blocked with 10% BSA or Streptavidin/Biotin Blocking kit (Vector) in the case of the MOMA-1 biotinylated antibody. After washing with PBS, sections were stained with the primary antibodies ON at 4°C, followed by a 60-min incubation period with Streptavidin-BV-421 (BioLegend) for MOMA-1 antibody. Sections were mounted with ProLong Gold antifade reagent (Thermo Fisher Scientific) and images were acquired on a Zeiss LSM780 confocal microscope equipped with 488-, 561-, and 633-nm lasers. Images were analyzed with Imaris software.
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