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464 protocols using facsaria 3 flow cytometer

1

Isolation and Characterization of Pancreatic Cancer Stem Cells

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Cancer stem-like cells from BxPC3 cancer cell line were labelled using the ALDEFLUOR assay kit according to the manufacturer’s recommendations (StemCell Technologies). The enriched subpopulation of CSCs was characterized using a FACSAria III flow cytometer (Becton Dickinson).
To analyse CSC markers treated and not treated BxPC3 CSCs were disaggregated by tryple and washed twice in PBS supplemented with 1% bovine serum albumin (Sigma-Aldrich). The cell surface Fc receptor was blocked using IgG (Santa Cruz Biotechnology) on ice for 15 min. Cells were stained for 30 min at 4 °C with anti-CD44-PE and anti-CD326 FITC and CxCR4-APC monoclonal antibodies (BD Biosciences). After washing, cells were analyzed using a FACSAria III flow cytometer (Becton Dickinson).
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2

Apoptosis and Cell Cycle Analysis

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Apoptosis was detected using an Annexin V-FITC Apoptosis Detection Kit (Koma Biotech, Seoul, South Korea). Briefly, cells transfected for 48 h were harvested through trypsinization, rinsed in PBS, and resuspended in 1× binding buffer before being incubated with 1.25 μL of Annexin V-FITC solution at 22–25 °C for 20 min in the dark, stained with 10 μL propidium iodide (PI; Sigma-Aldrich), and analyzed using a FACSAria III flow cytometer (BD Biosciences).
Apoptotic cells were evaluated using Hoechst 33342 and PI staining. The transfected cells were fixed in 4% paraformaldehyde (Biosesang) for 10 min and permeabilized with 0.2% Triton X-100 (Sigma-Aldrich) in PBS for 20 min. The cells were then treated with Hoechst 33342 (10 μg/mL; Invitrogen) for 10 min, stained with PI (20 μg/mL; Sigma-Aldrich) for 20 min, and observed using an Olympus IX71 microscope (Olympus).
To analyze the cell cycle, transfected cells were collected, fixed using 70% ethanol for 3 h at 4 °C, washed in PBS, and stained using 200 μL PBS containing 10 μg/mL RNase A, 1% Triton X-100, and 30 μg/mL PI (Sigma-Aldrich) for 30 min in the dark. The proportion of cells at each stage of the cell cycle was determined using a FACSAria III flow cytometer (BD Biosciences). Experiments were performed in triplicate.
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3

Multiparametric Flow Cytometry Profiling

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For ABCs detecting, PBMCs/B cells to be detected were incubation with FcR blocking reagent (Miltenyi Biotec) for 10 minutes at 4 °C, then stained with BV421 anti-CD11c (BioLegend) and percp-Cy5.5 anti-CD19 (BioLegend) at 4 °C for 30 minutes. For intracellular staining, cells were surface stained, fixed using eBio fix/perm kit (eBioscience), washed and stained with PE-Cyanine7 anti-T-bet (BioLegend) in 1 × eBio fix/perm buffer for 1 hour at 4 °C. Mouse IgG1 kappa Isotype Control, PE-Cyanine7 (eBioscience) was used as isotype control for T-bet staining.
For RNASE2 detecting, PBMCs to be detected were incubation with FcR blocking reagent (Miltenyi Biotec) for 10 minutes at 4 °C, then stained with APC anti-CD14 and viability dye efour 506 (Invitrogen) at 4 °C for 30 minutes. For intracellular staining, cells were surface stained, fixed with fixation/permeabilization solution (Cytofix/Cytoperm kit, BD), washed and stained with RNASE2 antibody (Invitrogen) in 1× Perm/Wash buffer for 1 hour at 4 °C, then stained with AlexaFlour 488 Goat anti-rabbit IgG (FCMACS). Cells stained with CD14 and AlexaFlour 488 Goat anti-rabbit IgG were used as isotype control for RNASE2 staining.
Then Cells were analyzed on a BD FACSAria III flow cytometer (BD Biosciences) using FACSDiva software. Cells were analyzed on a BD FACSAria III flow cytometer (BD Biosciences) using Flowjo VX software.
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4

Glioma Sphere Formation and Cell Counting

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As previously described9 (link), 50, 100, 200, 500 and 1,000 cells were separately sorted into each well of 96-well plates in at least eight replicates by a BD FACSAria III flow cytometer, and then cultured in the GSC medium in the presence or absence of indicated inhibitors or dimethylsulphoxide control for 6 days. Sphere size was then observed at day 6 using a Nikon inverted microscope Eclipse Ti-U equipped with a digital camera.
For glioma sphere cell counting, 1,000 cells per well were sorted into a 96-well plate in at least eight replicates by a BD FACSAria III flow cytometer and then cultured in the GSC medium in the presence or absence of indicated inhibitors or dimethylsulphoxide as control for 6 days. Single cells were dissociated from glioma spheres with StemPro Accutase. Cell number of living glioma spheres was counted under a Nikon inverted microscope Eclipse Ti-U using a haematocytometer following the addition of 50% (vol/vol) Trypan blue (Invitrogen).
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5

IgG Binding to Surface MOG in HEK293 Cells

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To detect the binding of patient serum IgG to surface MOG transduced in HEK293 cells, we conducted fluorescence-activated cell sorting (FACS) analysis as previously described [19 (link)]. Briefly, the transfected HEK293T cells were trypsinized and resuspended in Dulbecco’s modified Eagle’s medium, 2% fetal bovine serum, 1 mM ethylenediaminetetraacetic acid (FACS buffer) at 1.0 × 106 cells/mL. The cells were centrifuged at 4 °C for 1 h. All further steps were carried out at 4 °C. Patient serum (diluted 1:50 in FACS buffer) was mixed with 1.0 × 105 cells (100 µL). After rocking for 1 h, the cells were washed, and bound IgG was detected using Alexa Fluor 647 mouse anti-human IgG1 Fc antibody (5 μg/mL, A-10631, Thermo Fisher Scientific, Waltham, MA, USA) for 30 min and analyzed using a BD FACS Aria III Flow cytometer (Becton, Dickinson and Company, Franklin Lakes, NJ, USA). An IgG binding index, calculated as the ratio of the median AF647 fluorescence of green fluorescent protein–positive cells to that of green fluorescent protein–negative cells, of ≥2.5 was considered positive [3 (link)].
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6

Quantifying Microbial Metabolic Activity

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The analysis of metabolic activity was based on the procedure described by Cyplik et al. (2013) [42 (link)]. Approximately 1 mL of the culture medium was taken for analysis after 24 and 168 h of incubation. The samples were centrifuged (5 min, 3500 rpm) to separate the microbial cells. After decanting the supernatant, the pellet was washed twice using 1 mL of phosphate buffered saline (Sigma-Aldrich) and centrifuged (5 min, 3500 rpm). Then, the cells were suspended in 250 μL of phosphate buffered saline (Sigma-Aldrich) and 1 μL of Redox Sensor Green dye from the BacLight ™ RedoxSensor ™ Green Vitality Kit (Thermo Fisher Scientific, Waltham, MA, USA) was added to each sample. The systems were incubated for 10 min at room temperature. Fluorescence in the stained samples was measured using a BD FACS Aria ™ III flow cytometer (Becton Dickinson, Franklin Lakes, NJ, USA). The percentage ratio of active population (Q2) was determined by gating point plots of median values of green fluorescence signals (FITC-A) versus medians of light scattering values (SSC-A) based on a comparison to a previously prepared negative sample that contained metabolically thermally inactivated dead cells.
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7

Analyzing Cardiac Myocyte Protein Expression

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Adult cardiac myocytes were isolated from healthy mice as described, fixed in 2% PFA in PBS for 10 min, incubated in 50mM glycine for 30 min to remove auto-fluorescence caused by PFA at 488nm, and subsequently stained for SPARC (polyclonal goat antibody, R&D systems, AF492, 5μg/ml) overnight at 4°C. The next day cells were initially incubated with a secondary donkey-anti goat-alexa 488 labeled antibody for 90min. at room temperature and some cells were subsequently stained for integrin beta1 (monoclonal rat antibody, BD, 553715, 0.5μg/ml) for 4 hours at room temperature and afterwards incubated with a secondary goat-anti rat-alexa 568 labeled antibody for 90min. at room temperature. Cells were visualized with confocal microscopy on a Zeiss LSM700 microscope (Leica) using the Zen software (Leica), or analyzed using a BD FACSAria III flow cytometer (Becton Dickinson (BD), San Jose, CA) and FlowJo software (Ashland, Oregon).
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8

Cell Cycle Analysis of HepG2 and HuH-7 Cells

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HepG2 or HuH-7 cells (5 × 105) were seeded in 6-wells plate in DMEM-F12 medium supplemented with 10% FBS, during 24 h. Next, medium was replaced for the different medium treatment (10% FBS control, 0% FBS control, AM-CM 1/2 or AM-CM 1/4). After 24 or 72 h, cells were washed twice with cold PBS and collected with trypsin-EDTA 0,05%. (Gibco) The cells were centrifuged for 5 min at 1500 rpm and then fixed in 70% cold ethanol overnight at −20 °C. Centrifugation was performed for 5 min at 1500 rpm at room temperature. The resulting cell pellet was treated with 10 μg/ml RNase A (Sigma) in PBS, at 37 °C for 30 min, and stained with 50 μg/ml propidium iodide (PI) (Sigma) during at least 2 h (RT) in the dark. The distribution of cells in different phases of cell cycle was examined using a BD FACSAria III flow cytometer (Becton Dickinson). The results were analyzed using the FlowJo software (Becton Dickinson, San José, USA). Each experiment was performed in triplicate.
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9

Isolation and Cryopreservation of Canine T Cells

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PBMC were first stained with the fixable viability dye eFluor 780 (Thermo Fisher Scientific, Carlsbad, USA) according to the manufacturer’s protocol to discriminate dead from viable cells. In a second step, they were incubated with a mixture of heat-inactivated normal serum derived from dog and rat (each 15% in PBS) to block unspecific binding of Fc receptors. Then, cells were incubated with anti-canine TCRαβ (clone CA15.8G7) hybridoma supernatant, for 15 min in the dark on ice. A PerCP/Cy5.5-conjugated goat-anti-mouse IgG secondary antibody (Biolegend, San Diego, USA) was used for detection. Sorting was performed using the BD FACSAria™ III flow cytometer (Becton Dickinson, Heidelberg, Germany). The sorting strategy is shown in Figure 1B. After exclusion of dead cells and doublets, TCRαβ+ T cells from the lymphocyte gate were sorted with a purity >99% (Re-analysis using the FlowJo™10 software (Treestar Inc., Ashland, OR, USA). Isolated TCRαβ+ T cells were cryopreserved in 90% FBS, 10% dimethyl sulfoxide (Sigma-Aldrich) and shipped on dry ice to the Institute of Pathology, Microbiology & Immunology of the UC Davis.
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10

Immunophenotyping of ZAP70 in B-cells

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Fluorescently labelled antibodies to CD5‐peridinin chlorophyll protein (PerCP)‐cyanine (Cy) 5·5 and CD19‐allophycocyanin (APC) were obtained from Becton Dickinson (San Jose, CA, USA). ZAP70‐Alexa Fluor 488 and Mouse IgG1 Alexa Fluor 488 antibodies were purchased from Caltag (Buckingham, UK). Frozen or fresh MNC were stained by adding CD5‐PerCP‐Cy5·5 and CD19‐APC, permeabilised with 8E reagent, which was kindly provided by Prof. Dario Campana at National Singapore University, and followed by ZAP70‐Alexa Fluor 488 staining. Cells were then analysed with a BD FACS Aria III flow cytometer and FACS Diva Software (Becton Dickinson, San Jose, CA, USA). The percentage of B cells positive for ZAP70 was determined by gating the CD19/CD5 population. The threshold was set at 20%, as described previously (Crespo et al, 2003; Richardson et al, 2006).
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