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10 protocols using anti cd5

1

Isolation and Characterization of B Cells from Peripheral Blood

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PB samples were obtained after written informed consent was received from participants prior to inclusion in the study according to the Declaration of Helsinki, and approval by the ethics committee of the Medical Faculty at the University of Duisburg‐Essen, Germany (BO‐10‐4380). B cells were isolated by Ficoll density centrifugation (density 1.077 g/ml, Pan BioTech, Aidenbach, Germany) followed by staining with anti‐CD3 (BD Biosciences, Heidelberg, Germany), anti‐CD5 (BioLegend, Koblenz, Germany), anti‐CD20, anti‐CD23, and anti‐CD27 (each BD Biosciences) antibodies. Stained cells were analyzed on a CytoFLEX S flow cytometer (Beckman Coulter, Krefeld, Germany) using CytExpert v2.4 (Beckman Coulter) or FlowJo v10.6.2 (BD Biosciences) software. RNAseq data were retrieved from (Budeus et al, 2021 (link)).
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2

Murine Immune Cell Phenotyping

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Antibodies and reagents used for experiments include anti-CD11c (N418), anti-CD11b (M1/70), anti-CD8a (53–6.7), anti-B220 (RA3–6B2), anti-CD49B (DX5), anti-CD25 (PL61), Streptavidin (405232), anti-CD4 (GK1.5), anti-CD45.2 (104), anti-CD62L (Mel-14), Ly-6C (AL-21), anti-IFN-γ (XMG1.2), anti-CD3 (145–2C11), Rat IgG1 Isotype control (RTK2071), anti-CD28 (37.51), anti-CD5 (53–7.3), anti-VISTA (MIH63), anti-T-bet (4B10), (BioLegend), anti-CD69 (H1.2F3), anti-RORgt (q31–378), anti-TCR V beta 11 (RR3–15), anti-Nur77 (12.14), (BD), anti-TCR V alpha 3.2 (RR3–16), anti-Foxp3 (FJK-16 s), Fc-block (anti-CD16/32) (2.4G2), (ATCC).
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3

Multicolor FACS and IHC Antibody Panel

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A full list of antibodies is provided in the Key Resource table (Table 1). The following antibodies were used for FACS analysis: Anti-mouse/human CD45R/B220, anti-CD23, anti-CD21/CD35 (CR2/CR1), anti-CD93 [AA4.1], anti-mouse IgM, anti-IgD, anti-CD45.1, anti-CD45.2, anti-CD3ε, anti-Ly-6G/Ly-6C(Gr-1), anti-CD11b, anti-TCRb, and anti-CD5 were all purchased from Biolegend. Anti-Mouse CD19 was purchased from BD Biosciences. Rabbit Anti-Ki67 (Novocastra), rabbit anti-cleaved caspase 3 (Cell signaling), rabbit anti-Phospho-Histone H3 (Ser10) (Cell signaling), rat anti-Pax5 (Biolegend), Guinea pig anti-Cytokeratin 8+18 antibody, and FITC rat Anti-mouse/human CD45R/B220 (BioLegend) were used for fluorescence immunohistochemistry. Anti-rabbit Alexa Fluor Cy3 (Jackson ImmunoResearch), anti-rabbit Alexa Fluor 647 (Jackson Immunoresearch), anti-rat Cy3 (Jackson Immunoresearch), and Alexa Fluor anti-guinea pig 647 secondary antibodies were used for in fluorescence immunohistochemistry. Notch2 (D76A6) XP (Cell signaling) and HRP-linked rabbit IgG (GE healthcare) secondary antibodies were used for western blot analysis.
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4

Multiparametric Flow Cytometry Analysis

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Fresh whole blood was incubated with surface antibody cocktail containing the following: anti-CD19, anti-CD20, anti-CD3, anti-CD5, anti-CD8 (cat. 302240, 302326, 300439, 300626, and 301048 from Biolegend, respectively) and anti-CD45 and anti-CD4 (cat. 555482 and 562658 from BD Biosciences, respectively) in TruCount tubes (BD) and fixed with 1x FACS/Lyse (BD) as previously described(9 (link)). Samples were acquired on a LSR II (BD) or an Aurora (Cytek Biosciences, Fremont, CA) instrument and analyzed using FlowJo v10 (RRID:SCR_008520).
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5

Murine Immune Cell Phenotyping

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Antibodies and reagents used for experiments include anti-CD11c (N418), anti-CD11b (M1/70), anti-CD8a (53–6.7), anti-B220 (RA3–6B2), anti-CD49B (DX5), anti-CD25 (PL61), Streptavidin (405232), anti-CD4 (GK1.5), anti-CD45.2 (104), anti-CD62L (Mel-14), Ly-6C (AL-21), anti-IFN-γ (XMG1.2), anti-CD3 (145–2C11), Rat IgG1 Isotype control (RTK2071), anti-CD28 (37.51), anti-CD5 (53–7.3), anti-VISTA (MIH63), anti-T-bet (4B10), (BioLegend), anti-CD69 (H1.2F3), anti-RORgt (q31–378), anti-TCR V beta 11 (RR3–15), anti-Nur77 (12.14), (BD), anti-TCR V alpha 3.2 (RR3–16), anti-Foxp3 (FJK-16 s), Fc-block (anti-CD16/32) (2.4G2), (ATCC).
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6

Malignant Cell Calcium Flux Assay

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Cells from non-trial patients underwent cell surface phenotyping by flow cytometry using anti-CD19, anti-CD5 (both BioLegend), anti-IgM (Dako), and appropriate isotype control antibodies. Signaling capacity was determined by measuring the proportion of malignant cells that were able to flux intracellular calcium (iCa2+) following treatment with F(ab')2 anti-IgM, as described previously (29 (link)) using a FACScan or FACS Calibur instrument (BD Biosciences). All flow cytometry data were analyzed using FlowJo (TreeStar).
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7

Isolation and Culture of Human cDC1 and cDC2 Subsets

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PBMCs were isolated from buffy coats or apheresis from healthy donors (Sanquin, Nijmegen, The Netherlands) using Lymphoprep (STEMCELL Technologies). Total CD141+ CLEC9A+ DCs (cDC1s) were MACS isolated from PBMCs using the human CD141 (BDCA-3) MicroBead kit (Miltenyi Biotec), followed by isolation of total CD1c+ DCs (cDC2s) using the human CD1c (BDCA-1)+ dendritic cell isolation kit (Miltenyi Biotec). A purity check of the subsets after isolation was performed by additional FACS staining and measured flow cytometry (BD FACSCanto II). The cDC1s were stained with anti-Clec9a (SONY Biotechnology) and anti-CD141 antibodies (BioLegend), cDC2s were stained with anti-CD11c (BD Biosciences) and anti-CD1c antibodies (Miltenyi Biotec). Further cDC2 subset isolation was performed by FACS sorting (BD FACS Aria II SORP) using anti-CD11c (BC Biosciences), anti-CD1c (Miltenyi Biotec), anti-CD5 (BioLegend), anti-CD163 (eBioscience), and anti-CD14 (BD Biosciences) antibodies. The four cDC2 subsets were gated according to the following markers: P1 (CD11c+ CD1c+ CD5+), P2 (CD11c+ CD1c+ CD5 CD163), P3 (CD11c+ CD1c+ CD5 CD163+ CD14), and P4 (CD11c+ CD1c+ CD5 CD163+ CD14+). Cells were cultured in X-VIVO 15 serum-free hematopoietic cell medium (Lonza) with an addition of 10% fetal bovine serum (Gibco), and 40 U/mL human granulocyte-macrophage colony-stimulating factor (hGM-CSF) (Immunotools).
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8

Comprehensive Antibody Panel for Cell Analysis

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Primary antibodies used in this study include anti-DYKDDDDK Tag (CST, D6W5B, # 15009), anti-CD36 (BioLegend, # 336206), anti-KIR3DL1 (BioLegend, # 312716), anti-anti-KIR3DL2 (R&D, # FAB2878A), anti-anti-KIR3DL3 (R&D, # FAB8919r), anti-KIR2DL2/L3 (BioLegend, # 312612), anti-CD122 (BioLegend, # 105912), anti-CD5 (BioLegend, # 364016), anti-CD25 (BioLegend, 302610), anti-CD272 (BioLegend, # 344510), anti-CD2 (BioLegend, # 300214), anti-CD28 (BioLegend, # 302912), anti-CD80 (BioLegend, # 305219), anti-CD45 (BioLegend, # 304012), anti-IL6ST (BioLegend, # 362006), anti-CD276 (BioLegend, # 351006), anti-CD47 (BioLegend, # 323124). These antibodies were used at 1:100 dilution in MACS staining buffer (Miltenyi).
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9

Comprehensive B Cell Immunophenotyping

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Bone marrow, spleen, mesenteric lymph node (mLN) and Peyer’s Patch (PP) cells were isolated as described previously (26 (link)). In brief, cells were stained with anti-B220 (BioLegend), anti-CD11b (BD Biosciences), anti-CD43 (eBioscience), anti-CD24 (BioLegend), anti-BP1 (eBioscience), anti-IgD (BioLegend), anti-IgM (BioLegend), anti-CD93 (eBioscience) and anti-CD23 (BioLegend) for B cell development staining. For B1 and B2 cell development staining, cells were stained with anti-B220 (BioLegend), anti-CD19 (BioLegend), anti-CD43 (eBioscience), anti-CD23 (BioLegend) and anti-CD5 (BioLegend). For FOB and MZB cell staining, cells were stained with anti-B220 (BioLegend), anti-CD19 (BioLegend), anti-CD21 (BD Biosciences) and anti-CD23 (BioLegend).Cells were stained with anti-B220 (BioLegend), anti-Gl7 (BioLegend), anti-CD95 (Fas) (BD Biosciences), anti-CD86 (BioLegend), and anti-CXCR4(BioLegend) for GC B cell staining and cells were stained with anti-B220 (BioLegend), anti-MHC II (eBioscience) and anti-CD86 (BioLegend) for B cell activation staining.
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10

Comprehensive Immune Cell Profiling

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Fresh whole blood was incubated with surface antibody cocktail containing the following: anti-CD19, anti-CD20, anti-CD3, anti-CD5, anti-CD8 (catalog nos. 302240, 302326, 300439, 300626, and 301048 from BioLegend, respectively) and anti-CD45 and anti-CD4 (catalog nos. 555482 and 562658 from BD Biosciences, respectively) in TruCount tubes (BD) and fixed with 1× FACS/Lyse (BD) as described previously (9 (link)). Samples were acquired on a LSR II (BD) or an Aurora (Cytek Biosciences) instrument and analyzed using FlowJo v10 (RRID:SCR_008520).
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