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67 protocols using dnmt1

1

Western Blot Analysis of Endometrial Cancer

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Endometrial cancer cells were lysed with cold lysis buffer, and proteins were extracted followed by quantification of protein concentration. Equal amounts of proteins from each group were purified with 10% SDS-polyacrylamide gels, and then transferred to a polyvinylidene difluoride (PVDF) membrane, followed by blockading of non-specific binding by incubation with 5% skim milk over 1 h. The membrane was next incubated with primary antibodies overnight at 4 °C, and then treated with horseradish peroxidase-conjugated secondary antibody for 1 h. The ECL reagent (Millipore Corp.) was used for detecting antibody-reactive bands. The housekeeping proteins α-tubulin or β-actin was used as loading control. Primary antibodies against POLD1, JNK, p-JNK, c-JUN, and FOSL1 were purchased from Santa Cruz Biotech (Dallas, USA); primary antibodies against PGK1, HSP90, ERK, p-ERK, AKT, p-AKT, DNMT1, DNMT3A, DNMT3B, and SPARC were purchased from Cell Signaling Technology (Boston, USA); primary antibodies against Bcl-xL, Mcl-1, and Bax were purchased from Abcam (Cambridge, UK).
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2

Antibody Validation for Signaling Pathways

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Antibodies to H3K27me3, JMJD3, p-Smad3, Smad3, p-AKT, AKT, p-ERK1/2, ERK1/2, Notch1, Jagged-1, UTX and DNMT1 were purchased from Cell Signaling Technology (MA, USA). Antibodies to fibronectin, α-SMA, collagen III, JMJD3, TGF-β1, Notch3 were purchased from Abcam (MA, USA). An antibody to Smad7 was obtained from Santa Cruz Biotechnology (CA, USA). An antibody to β-actin, PTEN and FBXW7 were obtained from proteintech (Wuhan, China). β-tubulin was purchased from Sigma-Aldrich (MO, USA). GSKJ4 was purchased from Selleck (Houston, USA). DMSO and other chemicals were obtained from Beyotime (Shanghai, China). Lipofectamine 3000 was obtained from Invitrogen-Thermo Fisher Scientific (CA, USA).
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3

Quantifying DNA Methylation Regulators

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Cells were plated in 15-cm dishes 24 h before treatment with 0.1% dimethylsulfoxide or compound (6-point, fivefold serial dilution). Cells were lysed with 4% SDS and homogenized using QIAshredder columns (Qiagen). Proteins were separated on 4–12% Bis-Tris gels (Invitrogen) and transferred to nitrocellulose membranes (Invitrogen). Membranes were blocked with 5% milk and probed with primary antibodies against DNMT1 (1:1,000, Cell Signaling Technology, 5032), DNMT3A (1:1,000, Cell Signaling Technology, 3598), DNMT3B (1:1,000, Cell Signaling Technology, 67259), Phospho-Histone H2A.X (1:1,000, Cell Signaling Technology, 9718), Histone H2A.X (1:1,000, Cell Signaling Technology, 2595) or Vinculin (1:100,000, Sigma, SAB4200080). After washing, membranes were probed with IRDye secondary antibodies (LI-COR), washed again and imaged using a LI-COR Odyssey CLx Imager.
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4

Western Blot Analysis of Protein Targets

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Western blots were performed as previously described [21] (link), using the following antibodies detecting: Akt (cat.# 4691, Cell signalling, dilution 1:1000), Dnmt1 (cat.# ab188453, Abcam; dilution 1:500), Dnmt3a (cat.# SC-20703, Santa Cruz; dilution 1:1000), Dnmt3b (cat.# PA1–884, Thermo Fisher; dilution 1:1000), Stat3 (cat.# SC-8019, Santa Cruz; dilution 1:500), P-Stat3 (cat.# 9145, Cell signalling, dilution 1:1000), Stat5 (cat.# 25656, Cell signalling, dilution 1:1000), P-Stat5 (cat.# 9359, Cell signalling, dilution 1:1000), mouse c-Met (cat.# SC-8057; Santa Cruz; dilution 1:500), c-Myc (cat.# SC-40, Santa Cruz; dilution 1:1000), Hsc-70 (cat.# SC-7298, Santa Cruz; dilution 1:10000), Lin28b (cat.# SC-293120, Santa Cruz; dilution 1:500), h-Ras (cat.# SC-520, Santa Cruz, dilution 1:1000) and β-actin (cat.# SC-130657, Santa Cruz; dilution 1:1000).
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5

Western Blot Analysis of Cellular Proteins

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Cells were lysed in lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% sodium deoxycholate, 0.1% SDS, 1% NP-40, and 2 mM EDTA). The resulting lysates were resolved by electrophoresis and transferred to polyvinylidene difluoride membranes (Millipore, MA, USA). Blots were probed overnight (14–16 h) at 4°C with primary antibodies diluted 1/500-1/1000, labeled for 1 h with secondary antibody conjugated to horseradish peroxidase, and developed with Clarity Western ECL Substrate (BioRad, CA, USA). Blots were probed with antibodies against mouse ERK (Cell Signaling, MA, USA #9101), DNMT1 (Cell Signaling, MA, USA #5119), and leptin (Santa Cruz, TX, USA #sc-842).
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6

Immunoblotting of Dopaminergic Markers

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This was performed as previously described [20 (link)] with antibodies against D2R (1:500, rabbit), dopamine transporter (DAT; 1:500, rabbit), tyrosine hydroxylase (TH; 1:1000, rabbit) (AB5084P, AB1591P and AB152, Merck Millipore, Billerica, MA, USA), signal transducer and activator of transcription 3α (STAT3α; 1:1000, rabbit), DNMT1 (1:1000, rabbit), DNMT3a (1:1000, rabbit) (nos. 8768, 5032 and 3598; Cell Signaling Technology, Tokyo, Japan), DNMT3b (1 μg/ml, rabbit), ERRγ (1:1000, rabbit) and β-actin (1:10,000, mouse) (ab16049, ab128930 and ab6276; Abcam, Cambridge, MA, USA).
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7

Western Blot Analysis of hADSCs

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The hADSCs were lysed on ice for 15 min using Radio Immunoprecipitation Assay (RIPA) lysis buffer (BeyoTime, Shanghai, China) supplemented with protease inhibitor cocktail (Roche, Basel, Switzerland). The protein concentration of the lysate was then measured using the BCA Protein Assay Kit (BeyoTime, Shanghai, China) according to the manufacturer’s protocol. Protein sample were subjected to SDS-PAGE and transferred to polyvinylidene difluoride membranes (Millipore, Billerica, United States), which were blocked with 5% fat-free milk and then incubated with specific primary antibodies overnight at 4°C An anti-rabbit-horseradish peroxidase (HRP) secondary antibody was added, and the staining was visualized using an enhanced chemiluminescence detection system (Millipore, Billerica, United States). The primary antibodies used in this study were as follows: SIRT6, RUNX2, SP7, COL1A1, NOTCH1, NOTCH2, NOTCH3, NOTCH4, JAG1, HEY1 (Abcam, Cambering, United Kingdom), HA, Flag, GAPDH (BeyoTime, Shanghai, China) DNMT1, Acetylated Lysine (Ac-K) (Cell Signaling Technology, Danvers, MA, United States).
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8

Western Blot Analysis of Protein Targets

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Western blotting was performed as previously described [20] (link). The primary antibodies and their final dilutions were as follows: vIL-6 (1∶500; Abbiotec), DNMT1 (1∶1,000; Cell Signaling), STAT3 (1∶1,000; Cell Signaling), phospho-STAT3 (1∶1,000; Cell Signaling), AKT (1∶1,000; Cell Signaling), phospho-AKT (1∶1,000; Cell Signaling), actin (1∶1,000; Santa Cruz Biotechnology), lamin A/C (1∶1,000; Cell Signaling).
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9

Epigenetic Regulation in Cell Lines

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Pelargonidin chloride was purchased from Alkemist labs (Costa Mesa, CA, USA). 5-aza-deoxycytidine (5-aza), Eagle’s basal medium, trichostatin A (TSA) and TPA were provided by Sigma-Aldrich (St. Louis, MO, USA). The CellTiter 96® AQueous One Solution Reagent (MTS) and luciferase activity assay kit were provided by Promega (Madison, WI, USA). Primary antibodies specific for actin, Nrf2, NQO1, and HO1 were provided by Santa Cruz Biotechnology (CA, USA). Specific antibodies for HDAC1, HDAC2, HDAC3, HDAC4 and HDAC6, DNMT1, DNMT3a and DNMT3b were provided by Cell Signaling Technology (Beverly, MA, USA). The TOPO TA Cloning Kit was provided by Invitrogen (Invitrogen, USA).
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10

Epigenetic Modulation of Cancer Cell Biology

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CGA was provided by J&K Scientific. Ltd (Beijing, China), was dissolved in sterile H2O, the solution filtered using a 0.22-μm filter, incubated at −20°C, and diluted with the cell culture medium. 5-Azacytidine was obtained from Melone Pharmaceutical Co. Ltd (Dalian, China), dissolved in sterile Dimethyl Sulfoxide (DMSO, Sigma), and incubated at −20°C. The cells in the CGA group were treated for 48 h with graded doses of CGA (0, 250, 500, and 1000 μM). The cells in the 5 -AZA group were treated for 48 h with varying doses of 5-AZA (0, 1, 5, and 10 μM), and vehicle DMSO was present at an equal concentration in the control group (CON). The antibodies for DNMT1, p21, MMP2, MMP9, and GAPDH were procured from Cell Signaling Technology, Inc. (Danvers, MA, USA). The antibodies against p53 were obtained from Proteintech Group, Inc. (Wuhan, Hubei, China).
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