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5 protocols using ab157464

1

Immunoprecipitation of Zfp281 in ESCs and EpiSCs

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Two 15 cm dishes containing comparable numbers of confluent ESCs and EpiSCs were harvested, and nuclear extracts were prepared as described previously (Costa et al., 2013 (link)). For immunoprecipitation, nuclear extracts of ESCs and EpiSCs were prepared and incubated with pre-bound 4 μg Zfp281 (Abcam, ab101318) or IgG (Millipore, PP64) antibodies with protein G-Agarose beads (#11243233001, Roche) overnight at 4°C. Immunoprecipitates were washed five times with IP buffer, eluted from the beads by boiling, and separated by SDS-PAGE. Western blot analyses were carried out using the following primary antibodies: Zfp281 (sc-166933, Santa Cruz, RRID:AB_10612046), Ep400 (Bethyl, A300-541A, RRID:AB_2098208), Trrap (Santa Cruz, sc-5405, RRID:AB_2209666), Chd4 (Abcam, ab70469, RRID:AB_2229454), Mbd3 (Abcam, ab157464), Suz12 (Abcam, ab12073), Oct4 (Santa Cruz, sc-5279, RRID:AB_628051), and P300 (Santa Cruz, sc-584, RRID:AB_2293429).
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2

Immunoprecipitation and Western Blot Analysis

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Cell extracts were prepared by incubating the cells in lysis buffer (50 mM Tris-HCl [pH 8.0], 150 mM NaCl, 0.5% Nonidet P-40 [NP40]) for 30 min at 4°C, followed by centrifugation at 13,000 rpm for 15 min at 4°C. The protein concentrations of the total cellular lysates were measured using the micro bicinchoninic acid (BCA) protein assay kit (Pierce Biotechnology, Rockford, IL, USA). For immunoprecipitation, 500 μg of protein was incubated with specific antibodies (2–3 μg) for 12 h at 4°C with constant rotation, followed by incubation with 30 μL of 50% protein A/G agarose beads for 2 h. Beads were then washed five times with PBS. The precipitates were boiled in 2× SDS-PAGE loading buffer for 10 min, and then resolved in 10% SDS-PAGE gels. The proteins in the gel were transferred to polyvinylidene fluoride membranes. For western blotting analysis, membranes were incubated with antibodies, including MTA1 (1:1,000, #5646, Cell Signaling Technology), ZEB2 (1:1,000, ab138222, Abcam), E-cadherin (1:1,000, #14472, Cell Signaling Technology), vimentin (1:1,000, #5741, Cell Signaling Technology), MBD3 (1:1,000, ab157464, Abcam), and HDAC1 (1:1,000, ab19845, Abcam), overnight at 4°C followed by incubation with a secondary antibody. Immunoreactive bands were visualized using western blotting luminol reagent (Santa Cruz Biotechnology).
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3

Protein Expression Analysis in AMI and CAD Tissues

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The AMI and CAD tissues were lysed using strong RIPA buffer containing Halt Protease Inhibitor Cocktails (Thermo Fisher Scientific, Waltham, USA). Protein concentrations were evaluated with a bicinchoninic acid assay kit (Beyotime, Nantong, China). Primary antibodies targeting to beta actin (ab8226, Abcam), UHRF2 (ABE1028, MilliporeSigma), TET3 (ab153724, Abcam), UHRF2 (ZBTB33, MilliporeSigma), TET1 (ab19198, Abcam), DNMT3B (ab2851, Abcam), NTHL1 (ab191413, Abcam), UHRF1 (ab213223, Abcam), MBD3 (ab157464, Abcam), and SMUG1 (ab192240, Abcam), were incubated with targeted proteins at 4°C overnight, followed by incubating with appropriate horseradish peroxidase-conjugated secondary antibodies. Detection of horseradish peroxidase was performed with the Super Signal West Pico Chemiluminescent Substrate (Pierce).
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4

Chromatin Immunoprecipitation Profiling Antibodies

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The following commercially available antibodies were used:
Anti-H3 (1:5.000, #61475), Anti-H3K36me3 (1:4.000, #61102), Anti-H3K36me2 (1:1.000, #39255), Anti-H3K36me1 (1:1.000, #61351), Anti-H3K4me3 (1:500, #61379) and anti-H2A (1:1.000, #39209) were from Active Motif. Anti-H3K27me3 (1:1.000, C15410069), Anti-H3K79me3 (1:1.000, C15310068), anti-H2A.Zac (2 µg/IP, C15410202-050) and Anti-H3K9me3 (1:1.000, C15410056) were from Diagenode. Anti-H4K20me3 (1:1.000, ab9053), Anti-H3 (1:30.000, ab1791), anti-MTA1 (1:1.000, ab71153 or 3 µg/IP, ab50209), anti-CHD4 (1:1.000 or 2 µg/IP, ab70469), anti-HDAC2 (1:5.000, ab124974) anti-RBBP4 (1:1.000, ab488), anti-RBBP7 (1:1.000, ab3535), Anti-H3K27ac (2 µg/IP, ab4729), anti-H2A.Z (1:3.000, ab4174), and anti-MBD3 (1:5.000, ab157464) were from Abcam. Anti-PWWP2A (1:1.000, NBP2-13833) from Novus (Acris). Anti-HA-HRP (1:40.000, 2999S) and anti-HDAC1 (1:20.000, 5356S) from Cell Signaling Technology. Anti-FLAG M2 (1:80.000 or 3 µg/IP, F1804) and anti-mouse IgG (3 µg/IP, I8765) from Sigma-Aldrich.
The following secondary antibodies were used:
Anti-rabbit IRDye 800CW (1:10.000, 926-32211) and anti-mouse IRDye 680RD (1:10.000 926‐68070) from LI-COR Biosciences. Anti-mouse-HRP (1:10.000, M114) from Leinco Technologies. Anti-mouse and anti-rabbit HRP-linked antibodies (1:10.000, NA931 and NA934) from VWR.
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5

Western Blot Antibodies for MBD3 and β-ACTIN

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The monoclonal antibodies used for western blotting were rabbit anti-MBD3 (ab157464; Abcam) and rabbit anti-β-ACTIN (A-2066; Sigma).
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