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26 protocols using gr 1 rb6 8c5

1

Quantification of Tumor-Infiltrating Immune Cells

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Portions of tumors and tumor draining lymph nodes (TDLN) were frozen in
OCT at −70 °C and sectioned with cryostat for immunofluorescence
or were used for cell isolation for subsequent FACS. The following monoclonal
antibodies (mAb) were used for immunofluorescence in frozen sections: CD8a
(53–6.7, BD Pharmingen), perforin (CB5.4, Abcam), CD11b (M1/70, BD
Pharmingen), Gr-1 (RB6-8C5, BD Pharmingen), C3b/iC3b/C3c (2/11, Hycult Biotech)
(18 (link)), RPS19 (ab-155994), CD33
(825601, Biolgend), CD11b (ab52478, Abcam) and C5aR1 (C85-2506, BD Pharmingen).
Apoptotic cells were detected with Anexin V (sc-1929). Secondary antibodies
included Alexa Fluor (AF) 488, Texas Red, and AF 633-conjugated goat anti-rat
antibodies (Invitrogen). Perforin-expressing CD8+ T cells and
MDSC (CD11b+Gr-1+) tumor infiltrates were
quantified with Nikon Elements Advanced Research image-analysis software; cells
were counted in entire tissue sections and mean values per 63x field were
calculated.
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2

Immunophenotyping of Hematopoietic Cells

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Primary antibodies used for IHC and flow cytometry were as follows: c-Kit (2B8; eBioscience), CD16/32 (93; eBioscience), VE-cadherin (eBioscience), c-Kit (R&D Systems), Sca-1 (E13-161.7; BioLegend), CD48 (HM48-1; BioLegend), CD150 (TC15-12F12.2; BioLegend), IL-7Rα (SB/199; BioLegend), endoglin (MJ7/18; BioLegend), CD4 (L3T4; BD), CD8 (53-6.72; BD), B220 (RA3-6B2; BD), TER-119 (BD), Gr-1 (RB6-8C5; BD), CD34 (RAM34; BD), Mac-1 (M/70; BD), Flt-3 (A2F10.1; BD), CD41 (MWReg30; BD), CD45.2 (104; BD), CD45.1 (A20; BD), GPIbα (Xia.G5; Emfret), Clec2 (AbD Serotec), and Thpo (Bioss). Secondary antibodies for IHC were Alexa Fluor 488–conjugated IgGs (Molecular Probes) or Cy3/Cy5/DyLight549/DyLight649-conjugated IgGs (Jackson ImmunoResearch Laboratories, Inc.). IHC specimens were treated with DAPI (Molecular Probes) for nuclear staining. Stimulatory rabbit anti–mouse CLEC-2 antibody was a gift of K. Suzuki-Inoue.
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3

Immunofluorescence Analysis of Lung Tissue

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Lung tissues were harvested and fixed in 4% paraformaldehyde overnight. The tissues were subsequently washed in PBS and dehydrated in in 30% sucrose overnight. The tissues were embedded in optimal-cutting-temperature (OCT) compound (Sakura Finetek) and then frozen at −80°C. Tissue blocks were cut into 20-μm-thick sections and permeabilized in cold acetone. The sections were blocked with serum-free protein block (Dako) and immunolabeled with antibodies against mouse CD3 (2A7; BioLegend), Gr-1 (RB6-8C5; BD Biosciences), CD169 (3D6-1.12; AbD Serotec), and laminin (rabbit polyclonal; Abcam). The slides were mounted with ProLong Gold antifade agent (Thermo Fisher). Images were acquired using a confocal microscope (Olympus FV3000) using a 10× and 20× (0.95-numerical-aperture [NA]) objective and processed using Imaris (v9.5; Bitplane).
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4

Characterizing Qβ-specific Plasma Cells Post Adoptive Transfer

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For FCM staining spleens of mice after adoptive transfer were isolated in RPMI supplemented with 2% FCS and antibiotics and a single cell suspension was prepared. Red blood cells were lysed using ACK buffer prior to staining. Fc receptors were blocked using an anti-CD16/32 antibody (2.4G2, BD). To discriminate Qβ-specific plasma cells (PCs) from Qβ-specific activated and CS B cells, surface immunoglobulins (Ig) of specific cells were blocked using unlabelled Qβ VLPs. PCs were further stained with and characterized as IgM (polyclonal, Jackson ImmunoResearch), IgD (11-26c (11-26), eBioscience), CD4 (H129.19, BD), CD8 (53-6.7, BD), GR1 (RB6-8C5, BD), CD11b (M1/70, BD), CD11c (HL3, BD) negative (all antibodies labeled with PE), and B220-PE-Cy7 (RA3-6B2, BD) low. To detect Qβ specific PCs by intracellular staining of specific Ig, splenocytes were permeabilized using FACS lysing solution (BD, 349202) containing 0.04% Tween20 and stained with Alexa Flour 488 labeled Qβ VLPs. The congenic marker Ly5.1 (antibody labeled with APC, A20, eBioscience) identified all transfer derived B cells.
Qβ VLPs were labeled with the Alexa Flour 488 protein labeling kit (Thermo Fisher Scientific, A10235) according to the manufacturer's instructions.
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5

Spleen and Lymph Node Single-Cell Analysis

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Spleen and lymph node samples were forced through 100 µm filters to prepare single-cell suspensions. Dead cells were removed by gradient centrifugation with lymphocyte M (Cedarlane, Burlington, NC, USA) and live cells were stained with surface antibodies for flow cytometric analysis. Data were collected in a FACSCalibur flow cytometer (BD Biosciences, San Jose, CA, USA) and analyzed using FlowJo software (Tree Star, Ashland, OR, USA). Antibodies used: Gr-1 (RB6-8C5, BD Biosciences, San Jose, CA, USA), CD11b (M1/70, eBioscience, San Diego, CA, USA), CD62L (MEL-14, eBioscience, San Diego, CA, USA), CD44 (IM-7, eBioscience, San Diego, CA, USA) and EpCAM (G8.8, eBioscience, San Diego, CA, USA).
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6

Immunophenotyping of Lymphoma and TAMs

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Lymphoma immunophenotype was assessed as previously described [22 (link)]. The following antibodies were used for staining: CD19-APC, B220 (CD45R)-FITC, IgM biotin, IgD-PE, and Streptavidin-APC/Cy7 (BD Biosciences, USA). Data were collected by a flow cytometer (BriCyteE6, Mindray Bio- Medical Electronics Co. Ltd., Shenzhen, China) and analyzed using FlowJo Version 10.1 software. For the analysis of tumor-associated macrophages, cell suspensions of lymph nodes were obtained by grinding and filtering tissues through 0.4-μm cell strainers (BD Biosciences, USA) in PBS. Cells were then transferred to a fresh tube for centrifugation at 1000× g for 5 min. The cell pellet was incubated in red blood cell lysis buffer (Lonza) for 1 min at room temperature, diluted in PBS, and centrifuged for 1000× g for 5 min. The cell pellet was incubated with fluorescent-conjugated antibodies (dilution 1:50 in PBS) for 15 min at 4 °C in the dark, washed, and analyzed by flow cytometry. The following antibodies were used: F4/80 (6F12) from Miltenyi; CD11b (M1/70.15.5) and Gr1 (RB6–8C5) from BD Pharmingen.
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7

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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8

Hematopoietic Cell Profiling in Mouse Tissues

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Hematopoietic stem and progenitor cell and lineage-positive cell profiling was perform on BM, spleen, and thymus of mice from each genotype. Antibodies (clones) used: CD3 (145-2C11) [BD: #553064], CD4 (H129.19) [BD: #553653], CD8 (53-6.7) [BD: #553033], Gr-1 (RB6-8C5) [BD: #553128], B220 (RA3-6B2) [BD: #553090], Ter119 (Ter119) [BD: #553673], Mac1 (M1/70) [BD: #553311], IL7Rα (A7R34) [eBiosceinces: #12-1271-82], cKit (2B8) [BD: #558163], Sca-1 (E13-161.7) [eBiosceinces: #17-5981-83], CD25 (7D4) [eBiosciences: 13-0252-82], CD44 (IM7) [BD: 559250], CD43 (S7) [BD: 561856], HSA (M1/69) [BD: #553262] and BP-1 (6C3) [BD: #553159], CD4 (GK1.5) [BD: #561830], CD8 (7D4) [eBiosciences: #12-0081-82], B220 (RA3-6B2) [BD: #561880].
Flow cytometric gating strategy is described in Supplementary Fig. 6.
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9

Bone Marrow and Spleen Cell Isolation

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Bone marrow cells were harvested from femurs and tibiae by crushing the bones with a mortar and pestle. The cell suspension was collected after filtering through 40 μ membrane filter (BD). These cells were used for surface staining after red blood cell (RBC) lysis treatment with Red Blood Cell Lysing Buffer Hybri-Max (Sigma). Spleens were crushed between two glass slides and isolated cells were used for surface staining with respective antibodies after RBC lysis. Surface staining was done with B220 (RA3-6132, BD), CD3 (145-2C11, BD), Gr-1 (RB6-8C5, BD), Mac1 (M170, BD), CD45.1 (A20, BD), and CD45.2 (104, BD). After surface staining with respective fluorescent antibodies, polychromatic flow acquisition was performed using a LSR II instrument (BD) at the University of Rochester Flow Cytometry Core. Flow data was analyzed using FlowJo software (version 10.0.7 Treestar, Ashland, OR).
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10

Flow Cytometry Analysis of Progenitor Cells

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Flow cytometry analysis and cell sorting of MPPs, CDPs, cDCs, and pDCs was performed as described previously 28 (link). Amplified progenitor cells were deprived of Flt3L for 1.5–2 h and stained for Flt3, c-kit, and Gr1. MPPs and CDPs were defined as Gr1Flt3−/loc-kithi and Gr1Flt3+c-kitint, respectively. Gating strategy for MPPs and CDPs is shown in Supporting Information Figure 1C. DCs were stained for CD11c, CD11b, and B220. cDCs were identified as CD11c+CD11bhiB220lo whereas pDCs were defined as CD11c+CD11bloB220hi. Gating strategy for cDCs and pDCs is shown in Supporting Information Fig. 3A. Flow cytometry and cell sorting were performed on a FACSCanto II and FACSAria I device, respectively (BD Biosciences). Sorted cells were either directly cross-linked for ChIP or lysed for RNA isolation. The following antibodies were used: Flt3 (CD135, A2F10), c-kit (CD117, ACK2), CD11c (N418), CD11b (M1/70), B220 (RA3–6B2), SiglecH (eBio440c) (all from eBioscience), and Gr1 (RB6–8C5) (BD Biosciences).
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