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8 protocols using facscanto 2 flow cytometer

1

Cell Cycle Synchronization of Intracellular Parasites

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Flow cytometric analyses was performed as described previously (Liu et al., 2020 (link)). Monolayers of HFF were infected with tachyzoites at MOI = 1. After 12 h, synchronization of cell cycle was performed with 80 μM pyrrolidine dithiocarbamate (PDTC, Cat #S1809; Beyotime) at 37°C and 5% CO2 for 8 h. Then the medium was replaced with culture medium in the presence of 5 μM of each compound. After 8 h, the extracellular parasites were removed by cold PBS washing, and the intracellular tachyzoites were isolated from host cells through a 27-gauge needle and purified with a 3-μm filter. After centrifugation at 4°C for 10 min at 1,000 × g, parasites were fixed with 70% ethanol at −20°C for 24 h followed by cold 2% FBS washing. Parasites were stained with propidium iodide (PI; Cat # PH0530, Phygene) at 37°C for 30 min in the dark and then were filtered with a 5-μm pore filter. Harvested parasites were detected on FACSCanto™II flow cytometer (Beckman Coulter, CA, United States), and the results were analyzed using FlowJo 7.6.1 software (FlowJo LLC, Ashland, OR, United States). At least 50,000 events were collected per sample.
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2

Cytotoxicity Evaluation of MIONs@PDA in HUMSCs

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Briefly, HUMSCs were obtained after normal deliveries following 38–40 week gestations. HUMSCs were cultured in Dulbecco’s modified Eagle medium (Gibco, Waltham, MA, USA) containing 10% fetal bovine serum (Gibco) and negative for mycoplasma contamination. All experiments were conducted using HUMSCs at passages 5–8. After reaching 80% confluency, various concentrations of MIONs@PDA (0, 10, 25, 50, 100, and 200 μg/mL) were added to the medium for 12 h. The Cell Counting Kit-8 (Sigma-Aldrich, St. Louis, MO, USA) assay was used to detect the cytotoxicity of MIONs@PDA. HUMSCs were stained with the Prussian blue iron staining kit (Solarbio, Beijing, China), according to the manufacturer’s instructions. The phenotype of HUMSCs was confirmed by the expression of surface markers (positive for CD44-fluorescein isothiocyanate (FITC) and CD105-phycoerythrin (PE), and negative for CD45-FITC) (all from BD Biosciences, San Jose, CA, USA) using a FACSC anto II flow cytometer (FC500; Beckman Coulter Brea, CA, USA), and the data were analyzed with the CXP software (Beckman Coulter). Differentiation capacity of the HUMSCs was assessed by inducing osteocyte and adipocyte differentiation using the StemPro Osteogenesis/Adipogenesis Differentiation Kit (Invitrogen, Waltham, MA, USA) and evaluated by Alizarin Red S, Oil red O, and Alcian blue staining, respectively.
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3

Huh7 Cell Apoptosis Assay

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Using PBS bufffer to collect and wash cell suspension (1 × 106 cells/ml) twice. Cells were stained with Huh7 PE (BD, USA), Huh7 7-ADD (BD, USA), Huh7 PE and 7-ADD together, PE and 7-ADD together. A negative control was processed in parallel. Then, measured cell apoptosis by FACSCanto II flow cytometer (Beckman, USA).
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4

Flow Cytometric Immune Cell Analysis

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The gating strategy was shown in the previous study [23 (link)]. Doublets were removed from the analysis by setting the gate on single cells on the FSC-area (FSC-A) vs. FSC-high (FSC-H) dot plot. Cell proliferation was calculated from singlets. Next, the lymphocytes or monocytes were gated based on FSC and SSC dot plots. Then, the gate included lymphocytes, and analyses of CD4+, CD8+, and FoxP3+ cells were performed. The second sample included CD5+, CD14+, MHCII+ cells, and the median fluorescence intensity (MFI) of ROS was calculated on that cell population.
Flow cytometric analysis was performed using a FACSCanto II flow cytometer and Kaluza 1.5 software (Beckman Coulter, Brea, CA, USA); 10,000 cells of each sample were acquired. Prior to multicolor staining, the compensation was set using single-positive cells for each color.
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5

Comprehensive Immunophenotyping of Lung Cancer

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Flow cytometry was performed using fluorescence-conjugates or specific mAb and their controls followed by species-specific conjugate (Supplementary Table 2) using a FACS CantoII flow cytometer (Beckman Coulter) or a LSRFortessa (Becton Dickinson) from the flow cytometer facility Tuebingen. Positive cells in percentage (%) were calculated as follows: Surface expression in percent obtained with the specific antibody—surface expression in percent obtained with isotype control. Platelets were preselected by CD41a+ and CD62P (resting) or CD62P+ (activated). Data analysis was performed using FlowJo software (v.10). In order to verify the reproducibility of our flow cytometry system, we performed a Bland–Altman analysis (Supplementary Fig. 8f). For immunophenotyping of PBMC subsets of lung cancer patients and healthy control donors were identified by counterstaining with CD3-PECy5 (BD biosciences, San Diego, CA), CD19-APC/Fire750, CD4-Pacific Blue, CD8a-BV605, CD56-PECy7, CD14-BV785, HLA-DR-BV650 (Biolegend, San Diego, CA) and CD16-FITC (invitrogen). PD-1 and PDL-1 expression as well as activation levels were analyzed using a PD-1-APC or PDL-1-APC and a CD69-PE antibody (BD biosciences), respectively. Isotype controls were obtained from BD biosciences. Dead cells were excluded from analysis with LIVE/DEAD™ Fixable Aqua (Thermo Fisher Scientific, Waltham, MA).
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6

Multiparametric Flow Cytometry Panel

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The following fluorochrome‐labeled monoclonal anti‐human antibodies were used to identify central and effector cells: CD3‐APC‐Cy7, CD4‐V450 (REA623), CD45RA‐PE‐Vio770 (REA562), CD196 (CCR6)‐APC (REA190), CD183 (CXCR3)‐VioBright FITC (REA232), CD194 (CCR4)‐PE (REA279) and PerCP‐Cy5.5 anti‐CXCR5 (all from Miltenyi Biotec, Bergisch Gladbach, Germany). Cells were stained for 30 min at 4°C, measured with a FACSCanto II flow cytometer and analyzed using Kaluza Analysis version 2.1 (Beckman Coulter Life Sciences). Supporting information, Figure S3 reports the gating strategy for central and effector cell phenotyping panel, while Supporting information, Table S1 summarizes the main cell subsets identified from the analysis.
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7

Multiparameter Flow Cytometry for Follicular T Cells

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The following fluorochrome‐labeled monoclonal anti‐human antibodies were used to identify follicular T cells: CD3‐APC‐Cy7, CD4‐V450 (REA623), CD45RA‐PeCy7, CD196 (CCR6)‐APC (REA190), CD183 (CXCR3)‐VioBright FITC (REA232) and CD185 (CXCR5) (all from Miltenyi Biotech). Cells were stained for 30 min at 4°C, measured with a FACSCanto II flow cytometer and analyzed using Kaluza Analysis version 2.1 (Beckman Coulter Life Sciences). Supporting information, Figure S3 reports the gating strategy for follicular T cell phenotyping, while Supporting information, Table S1 summarizes the main cell subsets identified from the analysis.
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8

Apoptosis and Cell Cycle Analysis

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Apoptosis was evaluated using an Annexin V/PI double staining kit (Merck, Germany) according to the manufacturer's instructions. Briefly, single cell suspensions were incubated with Annexin V solution and stained by propidium iodide (PI) solution for 10 min at room temperature. Then, the cells were harvested and analyzed with a Becton Dickinson FACS CantoII Flow Cytometer (Beckman Coulter, USA).
To analyze DNA content and cell cycle by flow cytometry, the cells were harvested, washed twice with PBS, and fixed with 70% ethanol. Immediately before flow cytometric analysis, the cells were washed twice in PBS and then stained for DNA content using 0.5 ml of 400 µl/ml PI (Sigma, USA) and 100 μg/ml RNAase A (Sigma, USA) in PBS and 38 mM sodium citrate pH 7.4. Data were again collected on a Becton Dickinson FACS Canto II Flow Cytometer.
Cell culture and L-leucine/L-glutamine uptake assays TE-1 cells were cultured in RPMI-1640 medium containing 10% v/v FBS, penicillin-streptomycin solution, and 1 mM sodium pyruvate and maintained at 37°C in 5% CO 2 [ 3 H].-L-leucine and [ 3 H]-L-glutamine uptake assays were performed as described previously [18, 19] .
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