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29 protocols using facscanto cell analyzer

1

Phenotypic Analysis of Regulatory T Cells

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Flow cytometric analysis was performed on freshly isolated and expanded Tregs using the BD FACSCanto™ cell analyzer (BD Bioscience, Oxford, UK) and analysed using FlowJo software (TreeStarInc, OR, USA). In short, cells were washed and stained with the listed mAbs in the Supplementary Table 3 for 30 min at 4°C. Appropriate isotype control antibodies were used for each sample. Following staining, cells were examined by flow cytometry.
Intracellular staining for FOXP3 was performed in accordance with the manufacturer's protocol (eBioscience). Expression levels of and IL-17 was assessed after activation of cells with phorbol myristate acetate (PMA, 5ng/ml, Sigma Aldrich, St Luis, MO, USA), Ionomycin (1μg/ml, Sigma Aldrich, St Luis, MO, USA) and Monensin (2μM, eBioscience, San Diego, CA, USA) for 4 hours. Subsequently, the intracellular staining for IL-17 was performed according to the manufacturer's protocol.
In the BRC CRF, flow cytometry, using CD4-PerCP/Cy™5.5, CD-25PE, CD8-APC was carried out on the BD FACSCanto™ cell analyzer (BD Bioscience). Intracellular staining for FOXP3-FITC was performed, as above, in accordance with manufacturer's protocol (eBioscience). Appropriate isotype controls and Fluorescence minus one controls were used to assign gates and analysis carried out, using the FlowJo software.
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2

Chemokine Secretion Profiling Protocol

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Chemokine secretion was measured using the LEGENDplex Human Proinflammatory Chemokine Panel (13-plex) kit following manufacturer’s guidelines. Samples were analyzed using a BD FACSCanto cell analyzer.
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3

Pluripotent Stem Cell Analysis

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EBs were dissociated using Accuatase Cell Dissociation reagent (Invitrogen), washed with PBS supplemented with 2% FBS, and filtered through a 70-µm cell strainer (Falcon; BD). Cells were treated with propidium iodide (Sigma-Aldrich) before analysis. Cells were stained with hCD45 (leukocyte common antigen), hCD71 (transferrin receptor protein 1), and hCD235a-PE (glycophorin A) from BD and analyzed by a FACSCanto cell analyzer (BD) using FACSDiva software (version 6.0; BD).
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4

Quantifying Protein Synthesis in FaDu Cells

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FaDu cells were reverse transfected with a siPOOL designed against NSUN6 or a scrambled control siPOOL (siTOOLs Biotech). After 48 or 72 h, cells were treated with OP-puromycin for an hour. Afterwards, the cells were collected, fixed and permeabilized. Using Click-it chemistry (Thermo Fisher Scientific), the OP-puromycin containing peptides were stained with Alexa Fluor 647 and analysed on a FACSCanto Cell Analyzer (BD Biosciences). Cycloheximide treated cells were used as a control.
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5

Cell Cycle Analysis by Flow Cytometry

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Cells were trypsinized with 0.25% trypsin-EDTA (cat. no. 25200-114; Invitrogen; Thermo Fisher Scientific, Inc.) and the suspended cell pellet was incubated with 70% ethanol (cat. no. 1000927; Sinopharm Chemical Reagent Co., Ltd., Shanghai, China) at 4°C. Following the thorough removal of ethanol, the cells were suspended in a proprium iodide (PI) staining solution (cat. no. P3566; Invitrogen; Thermo Fisher Scientific, Inc.) in the dark, at room temperature for 30 min. Flow cytometry was performed using a FACSCanto Cell Analyzer (V07300617; BD Biosciences, Franklin Lakes, NJ, USA).
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6

Isolation and Purification of Human B Cells and Monocytes

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Total PBMCs were isolated using Ficoll-Hypaque density gradient centrifugation. B cells (CD19 pan B dynabeads) and monocytes (CD14 dynabeads) were either depleted or enriched using an antibody-coated magnetic bead column separation technique (Life Technologies, Grand Island, NY, USA). Dynabeads CD19 pan B and CD14 are both uniform (4.5 μm diameter) superparamagnetic beads coated with a primary monoclonal antibody specific for the CD19 or CD14 membrane antigen mainly expressed on human B cells and monocytes, respectively. Cell purity for B cells was performed as follows using flow cytometry and was determined to be >90%. Cells were stained for CD3 APC (Clone UCHT1) and CD20 FITC (Clone: L27) (source for both antibodies: BD Biosciences, San Jose, CA, USA) and analyzed using a FACSCanto Cell Analyzer (BD Biosciences, San Jose, CA, USA). Cells were analyzed using a lymphocyte gate and purity was assessed as CD3CD20+ lymphocytes. For monocytes, purity was assessed by staining cells for CD3 APC (Clone UCHT1) and intracellular CD68 FITC (Clone Y1/82A) (source: BD Biosciences, San Jose, CA, USA) after permeabilization and fixing. The cells were analyzed using a monocyte gate and purity assessed as CD3CD68+ cells.
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7

Hypoxic Erythroid Maturation Analysis

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The erythroid cells at the EB stage were cultured for 1 week at 37 °C in 5% CO2/air. After 1 week, these cells were transferred to a hypoxic incubator set at 37 °C, 5% O2, and 5% CO2 for 3 weeks. Subsequently, the cells underwent FACS analysis (FACSCanto cell analyzer (BD) using FACSDiva software, version 6.0; BD), and Glycophorin A (BD Biosciences, cat. 340947) was used as a marker for the assessment of RBC production and maturation. For FACS analysis, erythroid cells were analyzed for N = 4 subjects for CMS, non-CMS and non-CMS with ARID1B-KD samples. Additionally, we tested multiple clones (3 clones) for each of the subjects to show interclonal differences between erythroid cultures prepared from each iPS cell line.
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8

Hypoxic Erythroid Cell Maturation

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Erythroid cells at the EB stage were cultured for 1 week at 37 °C in 5% CO2/air. After 1 week, these cells were transferred to a hypoxic incubator set at 37 °C, 5% O2, and 5% CO2 for 3 weeks. Subsequently, the cells were subjected to FACS analysis (FACSCanto Cell Analyzer (BD) using FACSDiva software, version 6.0; BD), and glycophorin A was used as a marker for the assessment of RBC production and maturation.
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9

Blood Cell Phenotyping by Flow Cytometry

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Blood was collected by cardiac puncture and erythrocytes lysed with RBC lysis buffer (eBioscience). Neutrophils, monocytes and lymphocytes were identified based on forward and side scatter using a FACSCanto Cell Analyzer (BD Biosciences).
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10

Blood Cell Phenotyping by Flow Cytometry

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Blood was collected by cardiac puncture and erythrocytes lysed with RBC lysis buffer (eBioscience). Neutrophils, monocytes and lymphocytes were identified based on forward and side scatter using a FACSCanto Cell Analyzer (BD Biosciences).
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