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40 protocols using cd11b

1

Single-Cell Immune Profiling Protocol

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The reagents used in this study were as follows: collagenase, Type IV (Gibco), Deoxyribonuclease I from bovine pancreas (Sigma-Aldrich), EDTA (Invitrogen), Erythromycin (Sigma-Aldrich), Gentamicin (Sigma-Aldrich), LB agar (Condalab), LiberaseTM Research Grade (Roche), Pierce protease inhibitor (Thermo Fisher Scientific), PBS (Dutscher), RPMI 1640 w/stable glutamine (Dutscher), and TSB (BD Bacto). Antibodies and dyes from Miltenyi Biotec include: anti-mouse CD3ε (clone 17A2), CD335 (clone REA815), CD19 (clone REA749), CD45 (clone REA737), CD11b (clone REA592), Ly6G (clone REA526), Ly6C (clone REA796), Viobility 405/452 fixable dye, REA Control-APC (clone REA 293), REA Control-FITC (clone REA 293), REA Control-PE-Vio 770 (clone REA 293), REA Control- APC-Vio 770 (clone REA 293), REA Control- APC-VioBlue (clone REA 293), and REA Control- APC-VioGreen (clone REA 293).
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2

Isolation and Characterization of Immune Cells

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Iscove's modified Dulbecco's medium, FBS, glutamine, penicillin/streptomycin, HEPES, G418, and PBS were purchased from Euroclone (Pero, Italy). Primer pairs were obtained from Primm Biotech (Milano, Italy). Dispase and DNase I were obtained from Gibco-Life Technologies (Monza, Italy) and Roche Applied Science, respectively. Goat serum was purchased from Vector Laboratories (Burlingame, CA, USA). Flow cytometry antibodies were purchased as follows: CD11b and Gr1 from Miltenyi Biotec, Bergisch Gladbach, Germany; CD11c, CD80, MHCII, CD4, CD8, CD25, CD44, and Foxp3 from eBioscience, San Diego, CA, USA. All other reagents were purchased from Sigma-Aldrich (Saint Louis, MO, USA).
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Isolation and Characterization of Human Macrophages

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Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation of buffy coat preparations from blood of healthy donors (DRK, Germany). Monocytes were isolated by plastic-adherence and cultured in the presence of M-CSF (50 ng/ml, R&D). 6 day later macrophages were detached with EDTA (1 mM, Sigma). Expression of surface markers CD68, HLA-DR (BD), CD163 (eBioscience), CD11b (Miltenyi Biotec) and SIRP-α (Biolegend) were evaluated by flow cytometry.
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4

Induced Regulatory T Cell Differentiation

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Naive CD4+CD25− T cells were isolated by magnetic depletion of cells labeled with a biotin-conjugated antibody cocktail (CD8α, CD11b, CD11c, CD19, CD45R, CD49b, CD105, MHCII, Ter-119 and TCRγδ; Miltenyi Biotec), anti-CD25 (eBioscience) and anti-biotin-microbeads (Miltenyi Biotec). For iTreg differentiation, 1×106 cells/well were cultured in 24 well plates pre-coated with 2 μg/ml anti-CD3 antibody (2C11; BD Biosciences) and supplemented with 2 μg/ml soluble anti-CD28 (37.51; BD Biosciences) and 10 U/ml IL2 (NIH) in the presence or absence of 10 ng/ml recombinant human TGFβ1 (R&D Systems) for 3 days.
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5

Characterizing Purity of Bone Marrow-Derived Macrophages

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The purity of the BMM population was determined via flow cytometry analysis. 1x106 cells were taken from the freshly harvested BMMs, processed and stained with the required antibodies according to the manufacturer’s protocol. The fluorescently labeled monoclonal antibodies (mAbs) that specifically recognize proteins expressed by macrophages were used for phenotypical characterization. The used two-color panel included two surface antigens, F4/80 (1:100, Miltenyi Biotec, Germany) and CD11b (1:100, Miltenyi Biotec, Germany). In this two-color immunofluorescence protocol, the samples were single stained with each antibody, and then stained using both antibodies. Data were acquired with a MACS-Quant device (Miltenyi Biotec, Germany) using the MACSQUANTIFY™ software (Figure 1A).
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Cardiac Fibroblast Isolation and RNA-seq

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For PostniCre-mT/mG gene expression and RNA sequencing experiments cardiac fibroblasts were isolated and the subjected to flow cytometry as previously described (Molkentin et al., 2017 (link)). Briefly cells were strained through a 70 μm cell strainer and then stained with CD11b (1:50 Miltenyi Biotec 130–113-800) and MEFSK4 (1:50 Miltenyi Biotec 130–120-802) in HBSS with Ca2+, Mg2+ and 2%FBS. This allows for the removal of contaminating CD11b cells. Cells were then sorted on an Aria II live cell sorter. For PostniCre-mT/mG experiments the same antibody scheme was used but the MEFSK4+ GFP and MEFSK4+ GFP+ populations were segregated to compare the populations. RNA isolation was then preformed using an RNAqueous Micro Kit which is specifically designed for low RNA yields. Gene specific amplification was used during cDNA synthesis to increase signal of target genes.
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7

Isolation and Characterization of Alveolar Macrophages

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Mice AMs were obtained as previously described [68 (link)], and their phenotype was analyzed. Briefly, bronchoalveolar lavage fluid (BALF) from C57BL/6 mice was collected by inserting a 22G needle cannula into trachea. Ice-cold PBS was slowly instilled into the lung, and then the lavage fluid was collected as BALF. The BALF was centrifuged and cell pellets were collected. Cells were cultured in RPMI 1640 complete medium for 6 h. Then, adherent cells were collected as AMs. For identification of AMs, cells were stained with antibodies of CD11c (Miltenyi, cat no: 130122939, Bergisch Gladbach, Germany), CD11b (Miltenyi, cat no: 130113806, Bergisch Gladbach, Germany), CD45 (BD, cat no: 561018, Franklin Lakes, NJ, USA) and siglec-F (Miltenyi, cat no: 130123816, Bergisch Gladbach, Germany) and analyzed by flow cytometry. For detection of CD206 and CD80 expression in AMs, these cells were stained with antibodies of CD206 (Biolegend, cat no: 141712, San Diego, CA, USA) and CD80 (Miltenyi, cat no: 130102883, Bergisch Gladbach, Germany), and analyzed through flow cytometry.
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8

Isolation and Characterization of Cardiac Mesenchymal Stem Cells

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cMSCs were isolated from sham-operated and HF mice (8 weeks’ post-MI) using primary explant cell outgrowth culture. Cell outgrowths from minced myocardial tissue were cultured in cMSC media (Dulbecco’s modified Eagle medium [DMEM]/Ham’s F-12 culture medium [Thermo Fisher Scientific–HyClone] supplemented with 0.2 mM l-glutathione, 10 ng/mL leukemia inhibitory factor, 10 ng/mL basic fibroblast growth factor, 10% fetal bovine serum, and 1% penicillin-streptomycin). Lineage-positive (Lin+) cells (CD5+, CD45R+, Cd11b+, Gr-1+, TER-119+; Miltenyi Biotec, #130-092-613), endothelial cells (CD31+; BD, #553372), and fibroblasts (discoidin domain receptor 2 positive [DDR2+]; LSBio, #LS-C255961) were depleted from explant cultures by using antibody-conjugated magnetic microbeads. After depletion, LinCD31DDR2 cells were minimally expanded and further sorted by using a specific Sca1 antibody (eBioscience, #25-5981-81) and consequently enriched for Sca1+ cells. LinCD31DDR2Sca1+ cells were minimally expanded and used at cell passages 3 to 5 for all experiments. cMSCs were evaluated for their ability to differentiate into adipogenic, osteogenic, and chondrogenic lineages using standard differentiation protocols.9 (link) Lineage-specific gene expression was used to confirm successful differentiation as described.9 (link),28 (link)
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9

Isolation and Culture of Murine BmMSCs

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BmMSC were isolated from RPMI-flushed femurs and tibias of two male mice and isolated in complete isolation media (CIM) containing RPMI (Corning, 10-040-CV) with 10% fetal bovine serum (FBS, Atlanta Biologicals, S12450), 10% horse serum (HS, HyClone, SH30074.03), 1% 100 IU/mL penicillin G/100 µg/mL streptomycin (P/S, Corning, 30-002-Cl), and 12 µM final concentration of L-Glutamine (Corning, 25-005-Cl), as similar methodologies have been previously described [13 –15 (link)]. Once BmMSC were isolated, the cells were plated and cultured for expansion in complete expansion media (CEM) containing IMDM (Gibco, 12440–053), 10% FBS, 10% HS, 1% P/S, and 12 µM final concentration of L-Glutamine [14 (link), 15 (link)], which was followed by hematopoietic CD45 (Stem Cell Technologies, 19771) and CD11b (Miltenyi, 130-049-601 or 130-093-634) depletion, as recommended by [13 ], via magnetic negative selection at early passages 1–3. BmMSCs were passaged at 70–80% confluency. The majority of experiments were performed at passages 10–13 and are specified throughout the manuscript.
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10

Magnetic cell separation of LPMCs

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Colonic LPMCs were separated by MACS. LPMCs with specific CD antibodies were magnetically labeled with their respective magnetic beads (CD11c, #130-108-338; CD11b, #130-049-601; CD4, #130-049-201; Miltenyi Biotec). The cell suspension was loaded onto a MACS® LS Column (#130-042-401; Miltenyi Biotec), which was placed in the magnetic field of a MACS Separator (#130-042-301; Miltenyi Biotec). The MACS Separation Buffer contained a final BSA (Miltenyi Biotec) concentration of 0.5%. After cells were separated, they were analyzed for gene expression.
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