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6 protocols using dnmt1

1

Ginsenoside 20(S)-Rg3 Mechanism Study

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Ginsenoside 20(S)-Rg3 was obtained from Tasly Pharmaceutical Company (Tianjin, China) and dissolved at a concentration of 4 mg/ml in DMSO as a stock solution (stored at −20°C). It was then further diluted in cell culture medium to create working concentrations. The maximum final concentration of DMSO was less than 0.1% for each treatment, and was also used as a control. Antibodies including DNMT3A, DNMT3B, E-cadherin, N-cadherin, vimentin, and β-actin were from Cell Signaling Technology (Beverly, MA), FSCN1 was from Abcam (Cambridge, MA, USA), and DNMT1 was from Active Motif (Carlsbad, CA, USA).
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2

Western Blot Analysis of EMT Regulators

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Total protein was collected from cells by RIPA lysis buffer containing protease inhibitors (Roche, Indianapolis, IN, USA) and 1 mM PMSF on ice. Protein concentration was measured using the BCA-200 Protein Assay kit (Pierce, Rockford, IL, USA). After heat denaturation at 100°C for 5 min, proteins were separated by electrophoresis on 10% SDS–PAGE gels and then transferred onto nitrocellulose membranes (Pall Life Science, NY, USA). The membranes were blocked with 5% non-fat milk at room temperature for 1 h, and then incubated overnight at 4°C with rabbit anti-human E-cadherin(1:1000, Cell Signaling Technology, Danvers, MA, USA), N-cadherin(1:1000, Cell Signaling Technology, Danvers, MA, USA), vimentin(1:500, Cell Signaling Technology, Danvers, MA, USA), DNMT3A (1:500, Cell Signaling Technology, Danvers, MA, USA), DNMT3B(1:500, Cell Signaling Technology, Danvers, MA, USA), DNMT1(1:1000, Active Motif; Carlsbad, CA, USA), FSCN1(1:100000, Abcam, Cambridge, MA, USA), and mouse anti-human β-actin(1:1000, Cell Signaling Technology, Danvers, MA, USA). After washing with TBST, the blots were incubated with horse radish peroxidase (HRP)-conjugated goat anti-rabbit or anti-mouse IgG. Blots were visualized using ECL reagents (Pierce, Rockford, IL, USA) by a chemiluminescence imaging system (Bio-Rad, Richmond, CA, USA).
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3

Chromatin Immunoprecipitation Profiling

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Confluent hESCs from a 100 mm dish were used for 2 immunoprecipitations. ChIP was performed using the SimpleChIP Plus Enzymatic Chromatin IP kit (Cell Signaling Technology, 9003S) according to the manufacturer protocols. The antibodies used for ChIP were: H3 (Cell Signaling Technology, 9003S), IgG (Cell Signaling Technology, 9003S), TET1 (Genetex, GTX627420), DNMT1 (Active Motif, 39204). DNMT3A (Abcam, ab2850), and DNMT3B (Novus Biologicals, NB100–56514). Primers for ChIP-qPCR are provided in Supplementary Table 3.
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4

Western Blotting Quantification of Cellular Proteins

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For western blotting19 (link), cells were lysed in Triton X-100 sample buffer and proteins separated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis. Proteins were blotted on a nitrocellulose membrane (Thermo Scientific).
The following primary antibodies were used at the indicated dilutions: SAMHD1 (Proteintech, 1:1000), β-actin (BioVision via BioCat, 1:2000), DCK (Santa Cruz, 1:500), CDA (Santa Cruz, 1:100), ENT1 (Abcam, 1:500), and UCK1 (Thermo Scientific, 1:1000), UCK2 (Thermo Scientific, 1:1000), RRM1 (Santa Cruz, 1:1000), RRM2 (Santa Cruz, 1:1000), OCTN1 (Abnova, 1:1000), cPARP (,1:2000), yH2AX (Cell Signaling, 1:2000), Chk2 (Cell Signaling, 1:1000), pChk2 (Cell Signaling, 1:1000), SAMHD1 (ProteinTech, 1:2000), TIF1β (Cell Signalling, 1:1000), pTIF1β (Cell Signaling, 1:1000), DNMT1 (Active Motif, 1:1000). Visualization and quantification were performed by using peroxidase-labeled secondary antibodies (Calbiochem) and enhanced chemiluminescence (SuperSignal West FEMTO Substrate; Thermo Scientific) or IRDye-labeled secondary antibodies (LI-COR Biotechnology) according to the manufacturer’s instructions. Band volume analysis was conducted by Odyssey LICOR. Uncropped scans of the blots are provided as Source Data file.
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5

Chromatin Immunoprecipitation Protocol for Epigenomic Analysis

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Chromatin immunoprecipitation (ChIP) assays were performed according to the manufacturer’s protocol using the Chromatrap Enzymatic ChIP-seq kit. Immunoprecipitations were performed overnight at 4°C using antibodies against H3K27ac (Abcam 4729), H3K4me1 (Abcam 8895), H3K4me3 (Abcam 8580), H3K9me3 (Abcam 8898), H3K27me3 (Active Motif 39157), DNMT1 (Active Motif 39204) and DNMT3A (Active Motif 39206). Rabbit IgG were used as control for ChIP and primers within a gene desert on chromosome 16 were used as a negative control for qPCR.
All ChIP experiments were performed in triplicates using two independent chromatin preparations. The immunoprecipitated DNA and the input DNA were analysed by real-time PCR using the ΔΔCt method and the primers are listed in Supplementary Table 3.
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6

Chromatin Immunoprecipitation Profiling

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Confluent hESCs from a 100 mm dish were used for 2 immunoprecipitations. ChIP was performed using the SimpleChIP Plus Enzymatic Chromatin IP kit (Cell Signaling Technology, 9003S) according to the manufacturer protocols. The antibodies used for ChIP were: H3 (Cell Signaling Technology, 9003S), IgG (Cell Signaling Technology, 9003S), TET1 (Genetex, GTX627420), DNMT1 (Active Motif, 39204). DNMT3A (Abcam, ab2850), and DNMT3B (Novus Biologicals, NB100–56514). Primers for ChIP-qPCR are provided in Supplementary Table 3.
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