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3 protocols using 5 aza 2 deoxycytidine

1

Methylation Analysis of pri-miR-130b

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The TSS of pri-miR-130b was found using the FANTOM5 web tool and shown on a UCSC (hg38) genome viewer (genome.ucsc.edu/cgi-bin/hgTracks?db =hg38&lastVirtModeType=default&lastVirtModeExtraState =&virtModeType=default&virtMode=0&nonVirtPosition=&position= chr22%3A21565713%2D21569713&hgsid=1120218429_QZUMREbGdSxow5PziSeV6J0NtJad), whereas a CpG island was identified close to the TSS using the MethPrimer software (urogene.org/cgi-bin/methprimer2/MethPrimer.cgi). Genomic DNAs were extracted using MiniBEST Universal Genomic DNA Extraction kit, following the manufacturer’s instructions (Takara Bio, Inc.). The extracted DNA was treated with sodium bisulfite using the EZ DNA Methylation- Gold kit (Zymo Research Corp.). Two sets of PCR primers, UMet-F/R and Met-F/R, were used to amplify the unmethylated and methylated DNA sequences, and their sequences are listed in Table 3. The relative levels of the methylated DNA regions near the TSS of pri-miR-130b were determined using an SYBR Green-based quantitative methylation-specific PCR, as described [14 (link)]. 5-Aza-2’-deoxycytidine (MedChemExpress) at a final concentration of 5 μM was added to the media to treat target cells 24 h prior to the extraction of the cervical cancer cell genome.
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Analyzing Cell Cycle and Apoptosis with DNA Methyltransferase Inhibitor

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KYSE-150 cells were incubated with different dosages of DNA methyltransferase inhibitor for 48 h before flow cytometry analysis. DNA methyltransferase inhibitor 5-Aza-2′-deoxycytidine was acquired from MedChemExpress (Monmouth Junction, NJ, USA) and fully dissolved in dimethylsufoxide (DMSO) at a concentration of 10 mM. Apoptosis was assessed using the Annexin V, 633 Apoptosis Detection Kit (Dojindo, Kumamoto, Japan). Cell cycle analysis was performed using the Cell Cycle and Apoptosis Analysis Kit (Beyotime; Jiangsu, China). Both assays were carried out and analyzed on a flow cytometer (Beckman Coulter) according to the manufacturer’s instructions. Data from the apoptosis assay were analyzed using FlowJo v10 (FlowJo, LLC). Cell cycle distributions were statistically determined by Modfit LT 3.2 software (Verity Software House; www.vsh.com; Topsham, ME).
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Isolation and Activation of CD4+ T-cells

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T-cells were obtained from lung, spleen, thymus, or tracheobronchial lymph nodes (tLN). Mouse naïve CD4+ T-cells (CD4+CD62LhiCD44) were sorted by Naïve CD4+ T-cell Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). Human CD4+ T-cells were sorted by CD4+ T-cell Isolation Kit (Miltenyi Biotec). The purity levels were above 95% detected by BD FACSCelestaTM. For in vitro experiments, mouse CD4+ T-cells were cultured in RPMI 1640 medium (Corning, Manassas, VA, USA) supplemented with 10% FBS, and 1% penicillin-streptomycin, and then stimulated by anti-CD3 (precoated, 5 μg/mL; BD Biosciences) and anti-CD28 (1 μg/mL; BD Biosciences) for 3 h. For TH2 cell differentiation, naïve CD4+ T-cells were cultured under the following conditions: mIL2 (10 ng/mL; BD Bioscience), mIL4 (50 ng/mL; BD Bioscience), and anti-IFN-γ (10 μg/mL; BD Bioscience) with anti-CD3 (precoated, 5 mg/mL) plus anti-CD28 (1 mg/mL; BD Bioscience) for 5–7 days. Human CD4+ T-cells were stimulated by PMA (50 ng/mL; Sigma) and ION (500 ng/mL; Sigma) for 3 h. In pharmacologic inhibition experiments, T cells were pretreated with 5-aza-2′-deoxycytidine (1 μg/mL; MedChemExpress, Monmouth Junction, NJ, USA) and then stimulated with anti-CD3 (precoated, 5 μg/mL; BD Biosciences) and anti-CD28 (1 μg/mL; BD Biosciences) for 3 h.
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