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11 protocols using h3 ab1791

1

Chromatin Immunoprecipitation (ChIP) Analysis of Liver Samples

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Chromatin immunoprecipitation (ChIP) analysis was performed according to our previous publication [25 (link)]. Crude chromatin preparations were isolated from approximately 200 mg frozen liver samples and were sonicated and precleared with salmon sperm DNA-treated protein G agarose beads (40 μL, 50% slurry, sc-2003, Santa Cruz Biotechnology, Santa Cruz, USA). The precleared chromatin products mixed with 2 μg of specific primary antibody (H3, ab1791, Abcam, Cambridge, USA; H3K4me3, ab8580, Abcam; H3K27me3, 17-622, Millipore, Darmstadt, Germany) overnight at 4 °C. We used normal rat IgG as a negative control. For capturing the immunoprecipitated chromatin complexes, we added protein G agarose beads again into the aforementioned mixture. Finally, we released DNA fragments from reverse cross-linking and quantified target gene fragments using with specific primers (Table 2).
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2

Western Blot Analysis of Pluripotency Markers

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For western blots, cells were lysed in RIPA buffer (50 mM Tris-HCl, pH 7.4, 250 mM NaCl, 2% Nonidet-P40, 2.5 mM EDTA, 0.1% SDS,0.5% DOC) supplemented with PIC and PMSF, resolved on 6%–10% SDS-PAGE (Mini-PROTEAN electrophoresis chamber, Bio-Rad), and transferred on PVDF membranes (Mini Trans-Blot apparatus, Bio-Rad) following manufacturer’s protocols. Membranes were blocked in 5% milk in PBS with 0.1% tween (PBST) and incubated overnight at 4°C, or for 1hr at room temperature with primary antibodies (Rinf 84546S, CST 1:1000; Nanog A300–397A, Bethyl Laboratories 1:2000; Oct4 SC-5279, SantaCruz 1:500; H3 ab1791, abcam 1:15000; Tet2 ab124297, abcam 1:1000; Flag 14739S, CST 1:1000; Actin AC-15, abcam 1:40000). Secondary antibody incubations (HRP-anti mouse, 401253, or anti rabbit, 401393, 1:5000, CalBiochem) were carried out for 1hr at room temperature. For quantifying Rinf protein levels in chromatin bound and soluble fractions of the cell, ESC lysate was fractionated as described before (Zhang et al., 2016 (link)). Each fraction was analyzed by western blot using anti-Rinf antibody. In all experiments Actin or H3 were used as loading controls.
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3

Western Blot Analysis of Pluripotency Markers

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For western blots, cells were lysed in RIPA buffer (50 mM Tris-HCl, pH 7.4, 250 mM NaCl, 2% Nonidet-P40, 2.5 mM EDTA, 0.1% SDS,0.5% DOC) supplemented with PIC and PMSF, resolved on 6%–10% SDS-PAGE (Mini-PROTEAN electrophoresis chamber, Bio-Rad), and transferred on PVDF membranes (Mini Trans-Blot apparatus, Bio-Rad) following manufacturer’s protocols. Membranes were blocked in 5% milk in PBS with 0.1% tween (PBST) and incubated overnight at 4°C, or for 1hr at room temperature with primary antibodies (Rinf 84546S, CST 1:1000; Nanog A300–397A, Bethyl Laboratories 1:2000; Oct4 SC-5279, SantaCruz 1:500; H3 ab1791, abcam 1:15000; Tet2 ab124297, abcam 1:1000; Flag 14739S, CST 1:1000; Actin AC-15, abcam 1:40000). Secondary antibody incubations (HRP-anti mouse, 401253, or anti rabbit, 401393, 1:5000, CalBiochem) were carried out for 1hr at room temperature. For quantifying Rinf protein levels in chromatin bound and soluble fractions of the cell, ESC lysate was fractionated as described before (Zhang et al., 2016 (link)). Each fraction was analyzed by western blot using anti-Rinf antibody. In all experiments Actin or H3 were used as loading controls.
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4

Polyclonal Antibody Generation and Characterization

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Rabbit polyclonal antibodies were raised against H4R3me2a and N‐acH4 by Eurogentec (Belgium). Additional details and characterization of these antibodies are provided in 46, 47. Other antibodies used were as follows: H4 (62‐141‐13; Millipore), H3 (ab1791; Abcam), Naa4051 (a gift from Qwei Zhai), and IgG (NB810‐56910; Novus Biologicals).
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5

Atorvastatin Modulates Wnt/β-Catenin Signaling

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Atorvastatin (344423) and 2,3,5-triphenyltetrazolium chloride monohydrate (TTC) (T8877) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Atorvastatin was dissolved with DMSO and then diluted with ultrapure water to the desired concentration. The final concentration of DMSO in the atorvastatin solution administered to the animals is 0.5%. The total RNA extraction kit (LS1040) was purchased from Promega Biotechnology Co., Ltd. (Beijing, China). SYBR (Q711) was purchased from Vazyme Biotech Co., Ltd. (Nanjing, China). Recombinant mouse sclerostin (SOST) protein (1589-ST), which can inhibit Wnt/β-catenin signaling pathway by antagonizing the binding of Wnt to its receptor and reducing the expression of downstream β-catenin [41 (link), 42 (link)], was purchased from R&D Systems (Minnesota, MN, USA). XAV939 (S1180), which can inhibit Wnt/β-catenin signaling pathway by degrading β-catenin, was purchased from American Selleck Biotechnology Co., Ltd. (China Branch, Shanghai). β-actin (20068) was purchased from Zen Bioscience Co., Ltd. (Chengdu, China). H3 (ab1791) and β-catenin (ab32572) were purchased from Abcam (Cambridge, UK). GSK3β (12456) and p-GSK3β (9322) were purchased from CST (Boston, USA).
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6

Histone Modification Antibody Protocols

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Antibodies that recognize histone modification(s), including H3K9me1 (ab9045), H3K9me2 (ab1220), H3K9me3 (ab8898), H3K4me1 (ab8895), H3K4me2 (ab32356) and H3 (ab1791), were purchased from Abcam Limited (Cambridge, UK). H3K9me3 (07-442) and H3K9Ac (06-942) were purchased from Upstate Biologicals, Inc. (Lake Placid, NY).
Other antibodies' information is indicated as below. Anti-Flag (F3165, F7425) and anti-BrdU (B2531) are from Sigma-Aldrich (St Louis, Missouri). Anti-Myc (ab9106) is from Abcam. Anti-GAPDH (abc-2003) is from Abclon lnc. (Seoul, Korea). Anti-cyclin B1 (sc-245) is from Santa Cruz Biotechnology (Santa Cruz, CA). Anti-phospho-cdc2Y15 (#9111) is from Cell Signaling Technology, Inc. (Danvers, MA). Antibody against phospho-Suv39h1S391 was raised in rabbit using a synthetic peptide, amino acids 387–397 protein (C-GLPGSPKKRVR) (AbFrontier, Seoul, Korea). The CDK1 inhibitor IVRO-3306 (217699) and CDK2 inhibitor II (219445) were purchased from Merck Millipore (Darmstadt, Germany), dissolved in dimethyl sulfoxide (DMSO).
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7

Antibody Characterization for Chromatin Modification

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Chemicals and reagents were obtained from Sigma (St. Louis, MO, USA), RPI (IL, USA) or Fisher Scientific (Pittsburgh, PA, USA). We used the following antibodies in this study: purified monoclonal Npm antibody [39 (link)], B4, H1A, Nap1 [40 (link),41 (link)]. Anti- β-tubulin antibody (clone E7) is from the Developmental Studies Hybridoma Bank at the University of Iowa. The following antibodies were from Millipore: H2A (07–146), H2A.Z (07–594), H4 (07–108), and H2A/H4S1ph (07–179). The following antibodies were from Abcam: H3 (ab1791) and H4R3me2s (ab5823). H2A/H4R3me1 and H2A/H4R3me2s antibodies were used as described [42 (link)].
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8

Antibody Sourcing and Validation

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All antibodies used in the experiments were purchased. Actin (AF5003, 1:1000) and LMNB1 (AF1408, 1:1000) were purchased from Beyotime; P21 (10355-1-AP, 1:1000) was purchased from Proteintech (Wuhan, China); PHGDH (66350, 1:1000), yH2AX (9718, 1:800) and Ki67 (9129, 1:400) were purchased from Cell Signaling Technology (Danvers, MA, USA); PSAT1 (53804, 1:1000) was purchased from Signalway Antibody (Greenbelt, MD, USA); PSPH (DF12711, 1:1000) was purchased from Affinity Biosciences (Cincinnati, OH, USA); H3 (ab1791, 1:1000), H3K4me3 (ab213224, 1:1000), H3K9me3 (ab176916, 1:1000), H3K27me3 (ab192985, 1:1000), H3K36me3 (ab282572, 1:1000) were purchased from Abcam (Waltham, MA, USA).
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9

Epigenetic Regulator Binding Kinetics

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Immunoblotting was performed according to standard protocols with the following antibodies; EZH2 (D2C9, Cell Signaling), EED (AA19, Millipore), SUZ12 (Ab12073, Abcam), CDYL (ab5188, Abcam), Actin (C-11, Santa Cruz), VAV2 (EP1067Y, Abcam), VAV pY174 (sc-16408-R, Santa Cruz), H3 (ab1791, Abcam), H3k27me3 (07-449, Abcam), STAT3 (F2, Santa dividing Rmax. These occupancy responses were plotted against the log concentration of EZH2-HIS as standard dose-response curves and a steady-state model was used to fit the points. The affinity constants were interpolated from 50% occupancy.
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10

Immunoblotting of Viral and Host Proteins

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Cell lysates were made by washing the monolayers with phosphate-buffered saline (PBS) followed by incubation in 2% sodium dodecyl sulfate (SDS). Following sonication, the proteins were separated by SDS-PAGE, transferred to a membrane (Immobilon®-P), and then probed with antibodies using the Western Star chemiluminescent detection system (Applied Biosystems) using the following antibodies: VACV D8 and A14 (obtained from Yan Xiang, University of Texas, San Antonio (Meng et al., 2011 (link))), PKR D7F7 (#12297, Cell Signaling Technology), P-PKR E120 (ab32036, Abcam) actin (A2066, Sigma-Aldrich), IRF3 (D83B9, Cell Signaling Technology), H3 (ab1791, Abcam), STING (ab92605, Abcam).
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