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15 protocols using modfit software version 4

1

Cell Proliferation and Cell Cycle Analysis

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The Cell counting kit (CCK)-8 assay (Dojindo Molecular Technologies, Inc.) was used to detect cell proliferation following transfection according to the manufacturer's protocol. After 48 h transfection, cells were seeded in 96 well plate at the density of 4×103 cells/100 µl per well, and proliferation was detected at 0, 1, 2, 3 and 4 days. CCK-8 reagent (10 µl medium/well) was added prior to detection and after incubation for 1.5 h at 37°C, and the absorbance was measured at 450 nm using a microplate reader. Absorbance at 630 nm was used as the control.
For the cell cycle assays, 3×105 cells/well were harvested from a 6 well plate and fixed in ice-cold 70% (v/v) ethanol for 24 h at 4°C. The cell pellet was collected following centrifugation at 500 × g for 10 min at 4°C and resuspended in PBS. Cells were then stained with a mixture of RNase (10 µg/ml) and propidium iodide (50 µg/ml; Beyotime Institute of Biotechnology) in sodium citrate containing 0.5% Triton X-100 for 20 min, in the dark and at room temperature. The cells were subsequently analyzed using a flow cytometer (Gallios, Beckman Coulter, Inc.). The ModFit software version 4.0 (Verity Software House, Inc.) was used for data analysis.
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2

Evaluating Osteoblast Cell Cycle Progression

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Passage 2 osteoblasts were cultured at 4×105 cells/dish in 100 mm dishes for 24 h. Osteoblasts were then synchronized and incubated with 10−8 M 99Tc-MDP, 10 ng/ml β-FGF or medium (high-glucose DMEM supplemented with 10% FBS and antibiotics) alone for 48 h. Each condition was replicated three times. Cells were then digested with trypsin, washed with PBS and collected by centrifuging at 500 × g for 5 min at room temperature. Pre-cooled ethanol (70%, 1 ml) was added to the precipitate and the cell suspension was fixed at 4°C overnight. Following centrifugation at 500 × g for 5 min at room temperature, the precipitate was resuspended in 3 ml PBS, passed through a 400-mesh screen and stained with 1 ml propidium iodide (PI) at 4°C for 30 min in the dark. The cell cycle was assessed by flow cytometry, and 3×104 cells were collected for each sample. Modfit software Version 4.0 (Verity Software House, Inc., Topsham, ME, USA) was used for data acquisition, processing, calculation of apoptotic cell proportion, and the determination of cell cycle distribution. The S-phase fraction (SPF) and proliferation index [proliferation index=(S + G2/M)/(G0/G1 + S + G2/M) ×100%] were used to evaluate the speed of proliferation.
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3

Cell Cycle and Apoptosis Analysis

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LNCaP and C4-2 cells (1×106) were trypsinized, washed twice with PBS and fixed in 70% ice-cold ethanol (Sangon Biotech Co., Shanghai, China) for 1 h at 4°C. The samples were centrifuged at 300 × g for 5 min at 4°C, the ethanol was removed and they were incubated with 100 mg/ml RNaseA (Sigma-Aldrich; Merck KGaA) for 30 min at 37°C. For cell-cycle distribution analysis, 400 ul PI solution (BestBio Co., Ltd., Shanghai, China) was added to the cells. The cells were vortexed and incubated in the dark for 30–60 min at 2–8°C. For cell apoptosis analysis, cellular DNA was stained with the Annexin V-FITC/PI Apoptosis Detection kit (cat. no. BB-4101-2; BestBio Co., Ltd., Shanghai, China). Briefly, the cells were centrifuged at 300 × g for 5 min at room temperature and resuspended in Annexin V Binding Buffer. A total of 5 µl FITC Annexin V was added to the suspension, they were then gently vortexed and incubated for 15 min at 2–8°C in the dark. The cells were then incubated with 10 µl of PI solution, gently vortexed and incubated for 5 min at 2–8°C in the dark. Cell-cycle distributions and cell apoptosis were determined by flow cytometry using a BD FACSCalibur system (BD Biosciences, Franklin Lakes, NJ, USA) and data was analyzed using the ModFit software version 4.1 (Verity Software House, Inc., Topsham, ME, USA).
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4

Ferroptosis Inhibitor Modulates NCTD-Induced Cell Death

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The SKOV3 and OVCAR-3 cells were seeded in 6-well plates at a density of 105 cells/well overnight. The SKOV3 and OVCAR-3 cells were then pre-incubated with or without 1 µM Fer-1 at 37°C for 1 h, followed by treatment with 10 or 20 µg/ml NCTD for an additional 24 h at 37°C. Subsequently, cell death was analyzed using an Annexin V/7-AAD double staining kit (cat. no. KGA1026; Nanjing KeyGen Biotech Co., Ltd.) according to the manufacturer's instructions. Briefly, the SKOV3 and OVCAR-3 cells were centrifuged at 1,000 × g for 3 min at 4°C and washed with PBS (Beijing Solarbio Science & Technology Co., Ltd.) thrice. The cells were then re-suspended using 500 µl 1X Annexin V Binding Buffer (cat. no. KGA1026; Nanjing KeyGen Biotech Co., Ltd.). Subsequently, 5 µl of the Annexin V/7-AAD reagent were added, and the cells were incubated for 10 min at room temperature. Following a 1-h incubation, cell death was determined using a BD FACSCalibur system (BD Biosciences), and data were analyzed using ModFit software version 4.1 (Verity Software House, Inc.). Annexin V/7-AAD cells were considered alive cells (Q4), Annexin V+/7-AAD cells were considered early apoptotic cells (Q3), and Annexin V+/7-AAD+ cells were considered late apoptotic and necrotic cells (Q2).
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5

Measurement of Cardiomyocyte Oxidative Stress

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Primary cardiomyocytes were cultured in six-well plates at a density of 106 cells/well for 24 h and were infected with Ad-miR-29a-3pi or Ad-NC (density, 107 viral genome particles) for 48 h at 37°C. The cells were collected and washed with PBS three times (5 min/time). Afterwards, the cells were incubated with ROS Fluorescent Probe-dihydroethidium (DHE; Vigorous Biotechnology Beijing Co., Ltd.) in serum-free DMEM:Ham's F12 Nutrient Mixture medium for 30 min at 37°C in darkness. Then, the cells were fixed in 4% paraformaldehyde for 30 min at room temperature and the slides were mounted. The fluorescence was examined by fluorescent microscopy (magnification, ×40; Olympus Corporation). To quantify the relative fluorescence, the cells stained with Probe-DHE were collected at a concentration of 2.5×106 cells/ml and analyzed using a BD FACSCalibur system (BD Biosciences) within 1 h of staining. Data were analyzed using ModFit software version 4.1 (Verity Software House, Inc.).
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6

Flow Cytometric Analysis of Cardiomyocyte Apoptosis

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Primary cardiomyocytes were cultured in six-well plates at a density of 106 cells/well for 24 h and infected with Ad-miR-29a-3pi or Ad-NC (density, 107 viral genome particles) for 48 h at 37°C. Then, the cells were collected and washed with PBS three times (5 min/time). To determine cell apoptosis, an Annexin V-FITC-propidium iodide (PI) Apoptosis kit (Invitrogen; Thermo Fisher Scientific, Inc.) was used. In brief, the cells were washed with 1X Annexin V Binding Buffer (140 mM NaCl, 2.5 mM CaCl2 and 10 mM HEPES/NaOH, pH 7.4) at a concentration of 2–3×106 cells/ml. Then, the Annexin V-FITC and PI buffer was added and incubated with the cells at room temperature for 15 min. After treatment, the cells were filtered using a 300-mesh filter and analyzed by a BD FACSCalibur system (BD Biosciences) within 1 h of staining. Data were analyzed using ModFit software version 4.1 (Verity Software House, Inc.).
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7

Cell Cycle Analysis by Flow Cytometry

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Exponentially growing cells were seeded into 6-well plates at a density of 4×105 cells/well and synchronized in serum-free RPMI-1640 for 16–24 h. Then, the medium was replaced with RPMI-1640 containing 10% FBS and antibiotics. Following incubation for 24 h, cells were harvested, washed with ice-cold PBS, and fixed with precooled 70% ethanol overnight at 4°C. The next day, the fixed cells were washed with ice-cold PBS and stained with 500 µl propidium iodide (PI)/RNase Staining Buffer (BD Pharmingen; BD Biosciences) for 30 min at room temperature in the dark. Cell cycle analyses were performed with a flow cytometer (BD Biosciences). Cell cycle was analyzed using the ModFit software (version 4.1; Verity Software House, Inc.). The experiments were repeated three times.
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8

Evaluating β-elemene's Cell Cycle and Apoptosis Effects

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SiHa cells (1×106) were exposed to different concentrations of β-elemene (0, 20, 30 and 40 µg/ml) for 48 h and harvested. The cell cycle was investigated using a Cell Cycle Detection kit (Nanjing KeyGen Biotech Co., Ltd., Nanjing, China). Briefly, SiHa cells were washed with PBS and then fixed with 70% ethanol at 4°C for 30 min. Following this, the cells were suspended in 300 µl PBS and incubated with propidium iodide (PI; 20 mg/ml) and RNase (1 mg/ml) for 30 min. Cellular DNA was stained with propidium iodide (Nanjing KeyGen Biotech Co., Ltd.). Cell cycle distributions were determined by flow cytometry using a BD FACSCalibur system (BD Biosciences) and data was analyzed using the ModFit software version 4.1 (Verity Software House, Inc., Topsham, ME, USA). An Annexin V-FITC Apoptosis Detection kit (Nanjing KeyGen Biotech Co., Ltd.) was used to investigate cellular apoptosis. SiHa cells were washed with PBS and resuspended in 500 µl binding buffer. Annexin V-fluorescein isothiocyanate (5 µl) and PI (5 µl) were added to the samples, according to the manufacturer's protocol. Finally, the processed cells were subjected to flow cytometry and data were analyzed using the Cell Quest software version 5.1 (BD Biosciences). Each experiment was performed in triplicate.
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9

Apoptosis Detection in A549 Cells

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Annexin V-fluorescein-5-isothiocyanate apoptosis detection kit (BD Biosciences, San Jose, CA, USA) was used to detect the effect of miR-519d on A549 cell apoptosis using BD FACSCalibur system (SKU#: 8044-30-1001, BD Biosciences, Franklin Lakes, NJ, USA). For data analysis, the ModFit software version 4.1 (Verity Software House, Inc., Topsham, ME, USA) was used.
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10

Cell Cycle Analysis by Flow Cytometry

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AGS and SGC7901 cells (~1×106) cells were trypsinized, washed twice with PBS and fixed in 70% ice-cold ethanol for 1 h. The samples were centrifuged at 300 × g for 5 min at 4°C, the ethanol removed and they were exposed to 100 mg/ml RNaseA (Sigma-Aldrich; Merck KGaA, Darmstadt, Germany) for 30 min at 37°C. Cellular DNA was stained with propidium iodide (Nanjing KeyGen Biotech Co., Ltd., Nanjing, China). Cell-cycle distributions were determined by flow cytometry using a BD FACSCalibur system (BD Biosciences, Franklin Lakes, NJ, USA) and data was analyzed using the ModFit software version 4.1 (Verity Software House, Inc., Topsham, ME, USA).
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