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29 protocols using fcs express v4

1

Surface Phenotyping of Mesenchymal Stem Cells

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Surface phenotype of N‐ and PE‐hAMSC at p4 were investigated by flow cytometry following standard protocols as previously reported 33. Cells were acquired with a FACSCalibur (BD Biosciences, San Jose, CA, USA) and analysed with FCS express v4.07 (DeNovo Software, Los Angeles, CA, USA). Dead cells were gated out by propidium iodide staining (0.1 μg/ml; Sigma‐Aldrich, St Louis, MO, USA). Antibodies and suppliers used are described in Table 2.
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2

Characterizing Immune Cells in Murine Tumor Model

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Spleens and metastatic tumor lesions of FVBN202 mice were harvested when the animals became moribund and were then separately homogenized into a single cell suspension as described previously [11 (link)] and below. Splenocytes were then characterized using flow cytometry. Reagents used for flow cytometry include the following: anti-CD16/32 antibody (clone 93), FITC-CD3 (17A2); FITC-CD11b (M1/70); FITC-anti-mouse IgG (Poly4053); PE-GR-1 (RB6-8C5); PE-PD-1 (RMP1-30); PE-CD25 (3C7); PE-Ki67 (16A8); allophycocyanin-CD49b (DX5); allophycocyanin-CD62 ligand (MEL-14); allophycocyanin-Annexin V; PerCP/CY5.5-CD4 (GK1.5); PE/CY7-CD8α (53-6.7); Brilliant Violet 421-PD-L1 (10F.9G2); Brilliant Violet 605-CD45 (30-F11); and PI, all of which were purchased from BioLegend (San Diego, CA, USA). BD Horizon V450-Annexin V and FITC-FVS were purchased from BD Biosciences. Anti-rat neu antibody (anti–c-Erb2/c-Neu; 7.16.4), was purchased from Calbiochem. All reagents were used at the manufacturer’s recommended concentration. Cellular staining was performed as described previously by our group [11 (link)] or as recommended by the manufacturer (Ki67, FVS). Multicolor data acquisition was performed using a LSRFortessa X-20 (BD Biosciences). Data were analyzed using FCS Express v4.07 (De Novo Software, Glendale, CA, USA).
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3

T cell Phenotype Analysis by Flow Cytometry

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T cells were cultured with macrophages as described above. After 6 days of co‐culture, T cell phenotype was investigated by flow cytometry. Samples were stained with Zombie NIR Live/Dead Cell Kit (eBiosciences, San Diego, CA, USA) and then fixed with 0.5% methanol‐free formaldehyde (ThermoFisher, Waltham, MA, USA) for 15 min at room temperature (RT). The surface staining was carried out for 30 min at RT, using the following anti‐human antibodies: CD4 BV421 (1:50, RPA‐T4), CD45RA FITC (1:80, HI100) or CD45RA PerCP‐Cy5.5 (1:80, HI100), CD25 PerCP‐Cy 5.5 (1:40, M‐A251) or CD25 BV421 (1:100, M‐A251), CD119 PE (1:80, GIR‐208), CD183 PE‐Cy7 (1:40, 1C6/CXCR3). Cells were then permeabilized with 0.05% Saponin/100 mm Tris–HCl, pH 7.4, for 15 min. The staining of intracellular antigens was performed by incubating cells for 30 min with anti‐human antibodies FoxP3 PE‐CF594 (1:30, 259D/C7) or GATA3 AlexaFluor 647 (1:20, L50–823; both from BD Biosciences). Cells were acquired with a FACSAria (BD Biosciences) and analysed using FCS express v. 4.07 (DeNovo Software). Gating strategies are shown in Figures S2B (Th1 and Th2) and S2C (Treg) (see supporting information).
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Monocyte Differentiation into DC, M1, and M2 Cells

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Monocytes were differentiated towards DC, M1‐ and M2 macrophage‐like cells in the absence or presence of hAMSC (as described above). After culturing, the monocytes were collected by gently scraping cells from the wells. Surface phenotype was investigated by flow cytometry as previously reported 33, using cell markers described to be expressed by DC 43, 44, M1‐ 45 and M2 45, 46 macrophages. Cells were acquired with a FACSAria (BD Biosciences) and analysed with the FCS express v4.07 (DeNovo Software). Antibodies and suppliers used in this study are described in Table 2.
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5

Co-culture of T Cells with Mesenchymal Stem Cells

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Co‐cultures of T cells with N‐ and PE‐hAMSC were established in direct cell‐to‐cell contact. Around 105 hAMSC were seeded in 96‐well plates (Nunc, Roskilde, Denmark) in 150 μl of UltraCulture medium (Lonza, Basel, CH, Switzerland) and irradiated (30 Gy) to block proliferation. The day after, mixed lymphocyte cultures (MLC) were obtained by culturing 105 T lymphocytes and 105 γ‐irradiated allogeneic PBMC in 100 μl of UltraCulture medium (Lonza), in the absence (controls) or presence of hAMSC. T‐cell proliferation was assessed by 5‐ethynyl‐2′deoxyuridine (EdU) incorporation as previously described 38. Briefly, 10 μM EdU (Life Technologies, Carlsbad, CA, USA) was added on day 5 and incubated for 16–18 hrs. Incorporated EdU was detected by the Cu‐catalysed alkyne‐azide cycloaddition (CuAAC or ‘click') reaction of the ethynyl group with 2.5 μM 3‐azido‐7‐hydroxycoumarin (Jena Biosciences, Jena, Germany), in buffer solution (100 mM Tris‐HCl pH 8.0, 10 mM L‐ascorbic acid, 2 mM CuSO4) at RT for 30 min. The samples were acquired with a FACSAria (BD Biosciences) and analysed with FCS express v4.07 (DeNovo Software).
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Evaluating Cell Surface Marker Expression

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To evaluate the validity of some of the selectively expressed markers, cell surface expression levels of CD206/MRC1 and CD207/Langerin were assessed using flow cytometry through a similar gating strategy to the one presented in Fig. 1. Fluorescence minus one (FMO) controls were applied and net percentage positive cells was calculated by subtracting positivity for the FMO control. Results were analyzed using FCS Express v4.0 (De Novo Software, Los Angeles, CA).
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7

Rat Testis Cell Cycle Analysis

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The testes from rats treated with different concentrations of BPA for 24 h were removed, decapsulated and placed in PBS containing 0.1 mg/ml collagenase (Sigma, St Louis, MO). Then, the tubules were washed three times in PBS. Tubule cell isolation was performed by mechanical disaggregation in the presence of 0.1 mg/ml DNase (Sigma, St Louis, MO) using a 21G needle from different segments of the seminiferous tubules that were previously isolated in PBS. Then, the solutions were filtered by through a mesh with a pore diameter of 200 µm and another with a pore diameter of 70 µm. To analyze cell cycles, the individual cells were fixed in 70% ethanol overnight. The cells were pelleted and washed once with PBS. Then, the pellet was then dissolved in a cell cycle buffer containing 0.1% sodium citrate, 0.3% Triton X-100 (Sigma, St. Louis, MO, USA), 50 mg/ml propidium iodide and 50 mg/ml RNase A (Invitrogen, Carlsbad, CA, USA) dissolved in distilled water. The samples were analyzed within 10 min of buffer addition on a flow cytometer (FAScanto) and 10,000 gated events were acquired for each sample. All data were analyzed with the software FCS express V4.0 (De Novo Software, Los Angeles).
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Apoptosis Assay for BPA and NP in LNCaP Cells

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LNCaP cells treated with 100 µM BPA or 50 µM NP for 6 h were washed twice with PBS. After that, they were incubated with 5 µL of FITC-Annexin-V and 5 µL of propidium iodide for 15 min at room temperature in the dark. Then, 400 µL of binding buffer was added and analyzed by flow cytometry (FAScanto, BD Biosciences, Franklin Lakes, NJ, USA) and 10,000 gated events were acquired in each sample. All data were analyzed with software FCS express V4.0 (De Novo Software, Los Angeles).
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9

Isolation and Characterization of Tubule Cells

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Tubule cells isolation was performed by mechanical disaggregation in the presence of 0.1 mg/ml DNasa (Sigma, St Louis, MO) using a 21G needle from different segments of the seminiferous tubules isolation previously in PBS. Then, the solutions were filtered by through a mesh with a pore of 200 μm and then a pore of 70 μm of diameter. The filtered solutions were centrifuged for 3 min at 800 × g. Then the isolated cells were incubated in DMEM-F12 medium containing 3% BSA, for 30 min at 4°C. Primary antibody against ADAM17, or against ADAM10 coupled to phycoerytrin, was added diluted in blocking solution (1:250) and left to incubate overnight. The next day cells were washed three times with PBS and in the case of those incubated with the antibody against anti-ADAM17 they were dissolved in blocking solution with the corresponding secondary antibody conjugated with FITC (diluted 1:250) and incubated for one hour at 4°C. Then, cells were washed three times with PBS and the final pellet dissolved in PBS. The samples were analyzed by a flow cytometer (FAScanto) and 10,000 gated events were acquired in each sample. As controls, one autofluorescence sample, one sample with only primary antibody and one sample with only secondary antibody were analyzed. All date were analyzed with software FCS express V4.0 (De Novo Software, Los Angeles).
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10

Cell Cycle Analysis by Flow Cytometry

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After treatment, LNCaP and A2780 cells were fixed in 70% ethanol. The cells were then pelleted and washed once with PBS. Then, the pellet was dissolved in a buffer containing 0.1% sodium citrate, 0.3% Triton X-100 (Sigma), 50 mg/mL propidium iodide, and 50 mg/mL RNase A (Invitrogen, Carlsbad, CA, USA). The samples were then analyzed by a flow cytometer (FAScanto, BD Biosciences, Franklin Lakes, NJ, USA). Ten thousand gated events were acquired in each sample. All data were analyzed with software FCS express V4.0 (De Novo Software, Los Angeles, CA, USA).
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