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29 protocols using winmdi 2

1

Flow Cytometry Analysis of Pneumococcal Capsule

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Flow cytometry was applied to investigate the amount of capsular polysaccharide of S. pneumoniae D39 serotype 2. In principle, the flow cytometric analysis was carried out as described recently [70 (link)]. Briefly, pneumococci cultured in liquid media (CDM) were harvested, and 1 x 108 bacteria were incubated with an anti-serotype 2 specific antiserum (Statens Serum Institute, Denmark) (1:500 dilution in PBS) for 30 min at 4°C. Samples were then washed twice with PBS/0.5% FCS and stained with secondary goat anti-rabbit IgG coupled Alexa-Fluor-488 (Abcam). After 30 min incubation at 4°C bacteria were washed twice with PBS/0.5% and then fixed with 2% formaldehyde. Flow cytometry was conducted with a FACSCalibur™ (BD Biosciences, Heidelberg, Germany), and the CellQuestPro Software 6.0. (BD Biosciences) was used for data acquisition while analysis of the data was performed with the software WinMDI 2.9. The forward scatter (FLI-H) in the histograms (Fig 5B) demonstrated the increase in fluorescence intensity.
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2

Quantifying Mitotic Index using MPM-2 Antibody

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MPM-2 monoclonal antibody is widely used to assess mitotic disturbances. To assess the impact of drug treatment on cell division, we employed MPM-2 (anti-phospho-Ser/Thr-Pro) as a mitotic marker to evaluate the mitotic index of drug-treated cells [42 (link)]. Cells were initially placed in culture dishes (3 × 105), incubated overnight, and left untreated or treated with CDDO-dhTFEA for 24 h. The U87MG and GBM8401 cells were subjected to treatment with nocodazole as a positive control, which is known to induce metaphase arrest, and served as the positive control in the experiment. The cells were treated with 70% ethanol and kept at −20 °C for a minimum of 8 h to ensure fixation, stained with 200 µL of IFA-Tx buffer containing 0.1% sodium azide, 0.1% Triton X-100, 150 nM/L NaCl, 10 nM/L 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, and 4% fetal calf serum (FCS), along with an anti-mouse rabbit fluorescein isothiocyanate antibody (Serotec, Oxford, UK) and MPM-2 anti-phospho-Ser/Thr-Pro antibody for 1 h at room temperature in the dark. The cells were finally detected using FACSCalibur flow cytometry (BD Bioscience), and the functionality of the MPM-2 antibody was assessed in both the control and experimental groups using the freely available software, WinMDI 2.9 (BD Bioscience).
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3

Mitochondrial Membrane Potential Analysis

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The mitochondrial-membrane potential was analysed by JC-1 staining. Cells (3 × 105/well) were seeded in six-well plates and incubated with EGCG for 24 h. After treatment, the cells were harvested, washed with PBS, and resuspended in JC-1 staining solution (10 µM) at 37°C for 15 min. Subsequently, the cells were examined using a FACSCanto flow cytometer (Becton Dickinson). Data analysis was performed using the WinMDI 2.9 (BD; San Diego, CA, USA) software.
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Apoptosis Induction in Colorectal Cancer

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After treatment with various concentrations of ruxolitinib for 48, 72, 96 h, human CRC LS411N, SW620 cells were collected and washed with ice-cold PBS before staining with Annexin V-FITC for 15 min at room temperature in the dark followed by PI staining for 5 min at room temperature. The samples were analyzed with a BD FACSCanto flow cytometer (BD Biosciences). Data analysis was performed by the software WinMDI 2.9 (BD Biosciences). Human CRC LS411N and SW620 cells were treated with Z-VAD-FMK for 1 h followed by ruxolitinib treatment for another 48 h, and were collected and analyzed as aforementioned.
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5

Quantifying Reactive Oxygen Species

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CM-H2DCF-DA, dihydroethidine (DHE) and Mito-SOX fluorescent probes were used to measure the intracellular generation of hydrogen peroxide (H2O2), superoxide anions (O2·−) and mitochondrial superoxide, respectively. Briefly, 3 × 105 MDA-MB 435 cells were plated in 6-well plates and allowed to attach overnight. Cells were incubated with or without CDDO-Me and then incubated with 5 μM of H2DCF-DA for 30 min, 20 μM of DHE for 30 min, or 2.5 μM MitoSOX-Red for 20 min in the dark at 37°C. After washing with Hank's Buffered Salt Solution (HBSS) containing Ca2+ and Mg2+, cells were further processed for fluorescence-activated cell sorting (FACS) analysis using a FACScan system (BD Biosciences). Data were analyzed using WinMDI 2.8 software (BD Biosciences).
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6

Characterization of Mesenchymal Stromal Cells

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To confirm the stromal nature of cultured cells, fluorochrome-conjugated monoclonal cocktails antibodies with antigens CD90 and CD105 as MSCs markers and antigens CD45 and CD34 as hematopoietic cell markers with proper control isotypes and flow cytometry (Becton Dickinson, San Jose, CA, USA) were used (Sadighi et al., 2014) . In short, using Trypsin-EDTA 25.0%, cells were isolated from the flasks floor and for the confirmation of each antibody 105 cells were cast within a clean Eppendorf tube, as well as for each antibody an isotype control tube was considered. Then, cells were washed once with cold PBS containing 2%FBS. Finally, the stained cells were examined by flow cytometry and Win MDI 2.8 software (BD, Franklin Lakes, NJ, USA). Differentiation of MSC into bone cells and adipose tissue was done similar to that provided by Sidighi et al (Sidighi et al., 2014) .
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7

Apoptosis and Necrosis Assessment of Breast Cancer Cells

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Annexin FITC-conjugated (1 : 500) and propidium iodide (PI) fluorochrome-labeled cells were used to determine the nature of cell death (apoptosis or necrosis). After platting MCF-7 and MDA-MB-231 cells (3.5 × 105 cells/mL) in a 12-well plates, they were incubated with AVME at 10 and 20 µM for MDA-MB-231 cells and 11 and 22 µM for MCF-7, or solvent control (DMSO) for 24 h. Cells were then washed twice with cold PBS and suspended again in a buffer containing 10 mM HEPES (pH 7.4), 150 mM NaCl, 5 mM KCl, 1 mM MgCl2, and 1.8 mM CaCl2. The pellets were stained on ice in the dark for 15 min with a fluorescent probe solution containing 50 mg/mL PI and 1 mg/mL Annexin. The total percentage of cells experiencing apoptosis was demarcated as the sum of both early and late facets of apoptosis (Annexin V-FITC positive), lower and upper right quadrants in the two-parameter dot plots, as previously described by Robles-Escajeda et al. [26 (link)]. The WinMDI 2.9 software and the flow cytometer BD FACSVerse (Becton Dickinson, Franklin Lakes, NJ, USA) were used for analysis. Each experiment was repeated thrice.
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8

Annexin V/PI Staining for Cell Death

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The dead, necrotic, and apoptotic cells were analyzed by annexin V/PI double staining method, which was used to detect the externalization of phosphatidylserine (PS). Briefly, cells at the density of 4.5 × 104 cells/well were seeded into 6-well plates and treated with or without DKPs for 24 h. Subsequently, both floating and adherent cells were harvested by centrifugation at 1,500 rpm for 5 min, then re-suspended in 300 μL of 1X binding buffer, followed by 3 μL of annexin V-FITC and propidium iodide (PI) (Apoptosis Detection kit, Lead Gen, Taiwan) was added into each sample and incubated for 20 min at room temperature in the dark following the protocol recommended by the manufactures. Cells were analyzed by flow cytometry (FACS Calibur, Becton Dickinson, CA, USA) using WinMDI 2.9 software (La Jolla, CA, USA). The individual populations can be defined using quadrant gates, the number of cells in each quadrant indicated the following: Quadrant-1 (Q1): annexin V-/PI+ cells were considered as dead cells; Quadrant-2 (Q2): Annexin V+/PI+ cells were considered as late apoptotic and necrotic cells; Quadrant-3 (Q3): Annexin V+/PI cells were considered as early apoptotic cells; Quadrant-4 (Q4): Annexin V-/PI- cells were considered as healthy. Data were analyzed using FlowJo V12.1 software (Tree stat, Stanford, CA, USA).
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9

Cell Cycle Analysis via Flow Cytometry

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SW1990 stably expressing SATB1 shRNA or empty vector cells were incubated in six-well plates (5 × 104 cells/well). Forty-eight hours later, cells were fixed with 80 % chilled ethanol and then incubated with 0.5 % Triton X-100 solution containing 1 mg/ml RNase A (Qiagen, Germantown, MD, USA) at 37 °C for 30 min. Propidium iodide (PI) (Sigma) was added to each well at a final concentration of 50 μg/ml later, followed by a 30-min incubation in the dark. Cellular DNA content was analyzed using a FACS machine (Becton–Dickinson, Franklin Lakes, NJ, USA). Data were processed using WinMDI29 software (Becton–Dickinson).
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10

Cell Cycle Analysis of Cantharidin Treated MDA-MB-231 Cells

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Prior to analysis, serum was deprived for 24 h to synchronize cell cycle. Serum was then added back into the culture medium containing various doses of cantharidin (0, 2.5, 5, and 10 μM). After the treatments with cantharidin for 24 hours, MDA-MB-231 cells were fixed with 80% cold ethanol, and incubated with 0.5% Triton X-100 solution containing 1 mg/mL RNase A at 37°C for 30 min. Afterwards, propidium iodide (PI, Sigma) was added into each well at a final concentration of 50 μg/mL and the cells were further incubated for 30 min in the dark. Cell cycle progression was analyzed by a FACS (Becton Dickinson, USA). Data were processed using WinMDI29 software (Becton Dickinson).
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