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13 protocols using histone 3

1

Western Blot Analysis of Epigenetic Regulators

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Western blot analysis was performed according to standard protocol as previously described (Dudakovic, Camilleri, Xu, et al., 2015 (link)). Cells were lysed using RIPA buffer at indicated time points. Proteins were visualized using SuperSignal West Femto Reagent (Thermo Fisher Scientific) and imaged using the ChemiDoc Imaging System (BioRad). Antibodies and concentrations used for western blot analysis were as follows: Brd2 (Cell Signaling; Cat #D89B4 1:1000), Brd4 (Bethyl Labs; Cat #A301–985A; 1:2,000), Runx2 (in house; 1:3,000), Gapdh (Cell Signaling; Cat #51745; 1:5,000), H3K27Me3 (Cell Signaling; Cat #9733S, 1:1,000), H3K27Ac (Millipore; Cat #07–360; 1:1,000), Histone 3 (Millipore; Cat #05–982; 1:10,000).
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2

Histone Acetylation Analysis in Progenitor Cells

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Western blot analysis was performed using standard techniques. In brief, differentiating CD34+ progenitors were lysed in Laemmli buffer [0.12 mol/L Tris-HCl (pH 6.8), 4% SDS, 20% glycerol, 0.05 μg/μL bromophenol blue, and 35 mmol/L β-mercaptoethanol], sonicated, and boiled for 5 minutes. Equal amounts of total lysate were analyzed by 12% sodium dodecylsulfate polyacrylamide gel electrophoresis. Proteins were transferred to a polyvinylidene difluoride membrane (Millipore, Bedford, MA), incubated with blocking buffer (Tris buffered saline/Tween 20) containing 5% low-fat milk for 1 hour at room temperature before incubation with antibodies against acetyl-histone 3 (lysine 27) (Millipore, Billerica, MA) or histone 3 (Millipore, Billerica, MA) overnight at 4°C in a buffer containing Tris buffered saline/Tween 20 with 5% bovine serum albumin (BSA) (Sigma-Aldrich, Zwijndrecht, the Netherlands). Blots were subsequently incubated with peroxidase-conjugated secondary antibodies (Dako, Glostrup, Denmark) for 1 hour at room temperature. Chemiluminescence was used as a detection method according to the protocol of the manufacturer (Odyssey, Amersham Pharmacia, Amersham, UK).
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3

Western Blot Analysis of STAT1

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Cell lysates were collected in a buffered SDS solution (0.1% glycerol, 0.01% SDS, 0.1 m Tris, pH 6.8) on ice. Total protein concentrations were obtained with the Bio‐Rad DC assay (Bio‐Rad, Hercules, CA, USA). Proteins (20 μg) were then resolved by SDS‐PAGE and transferred to a polyvinylidene difluoride membrane. Western blotting was performed with antibodies (1:2000 dilution) for phospho‐S727 STAT1 (Cell Signaling Technology, Danvers, MA, USA; #9177), STAT1 (Cell Signaling Technology, #14994), Histone 3 (Millipore, #05–928), and corresponding secondary antibodies conjugated to HRP (Cell Signaling Technology). Antibody binding was detected with the Supersignal West Femto Chemiluminescent Substrate (Pierce Biotechnology, Rockford, IL, USA). Shown are data from averaged from 3 males, but studies were performed in females (n = 3 per group) or males (n = 3 per group) of each genotype in three independent replicate experiments, each containing 12 pooled replicate wells per group.
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4

Histone Extraction and Western Blot Analysis

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Cells and tissues were lysed in RIPA buffer. Histones were extracted as described below. Samples were subjected to western blot analysis as reported [20 (link),117 (link)]. Primary antibodies were: α-tubulin (T6074, Sigma-Aldrich), SMAD3 (C67H9, Cell Signaling, Danvers, MA, USA), pSMAD3 (C25A9, Cell Signaling), α-SMA (F3777, Sigma-Aldrich), VASP (3112, Cell Signaling), pVASP (Ser239) (3114, Cell Signaling), GUCY1B3, sGC1β (ab15484) (ab154841, Abcam), PKG-1 (3248, Cell Signaling), histone-3 (05-928, Millipore), Acetyl-Histone H3 (Lys14) (06-911, Millipore), pAKT (Ser473) (9271, Cell Signaling), AKT (9272, Cell Signaling), active β-catenin (05-665, Millipore), collagen-I (ab138492, Abcam, USA), and DKK1 (AF1096, R&D Systems). For quantification of immunoblot signals we used the Image Lab Software from Bio-Rad Laboratories.
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5

ChIP Assay with Histone3 and LSD1

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The EZ-Magna ChIP kit (EMD Millipore) was used to conduct the chromatin immunoprecipitation (ChIP) assays in accordance with the manufacturer’s protocol. After carrying out the above-mentioned cell treatments, the cells were lysed with Cell Lysis Buffer and Nuclear Lysis Buffer and sonicated to obtain chromatin fragments. Next, the lysates were immunoprecipitated with Magnetic Protein A Beads conjugated with Histone3 (Millipore) or IgG (Millipore) as a control. Western blot assay was performed to detect the enrichment of LSD1, H3K27me1 (Millipore), H3K4me2 (Millipore), and DNMT1 (Millipore) in the precipitated protein complex.
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6

Protein Extraction and Western Blot Analysis

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Cells were incubated with 100 μl of radioimmunoprecipitation assay (RIPA) buffer containing protease and dephosphatase inhibitors (Santa Cruz Biotechnology, Dallas, TX, USA) for 30 min at 4°C and then centrifuged at 16,000 × g for 20 min. Total protein was then subjected to immunoblotting using antibodies against Cleaved caspase 3 (1:500), H3K9me2 (1:200; Merk), Histone 3 (1:1,000; Merk), Nestin (1:500), NF-M (1:500), MAP-2 (1:500), GAPDH (1:1,000; Santa Cruz Biotechnology), or β-actin (1:5,000; Sigma-Aldrich), followed by the appropriate horseradish peroxidase-conjugated secondary antibodies (1:10,000; Jackson ImmunoResearch Laboratories, West Grove, PA, USA). Details of primary and secondary antibodies are summarized in Supplementary Tables 3 and 4.
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7

Western Blot Analysis of Proteins

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Protein samples were separated on 12% SDS-polyacrylamide gels and transferred to PVDF membranes. Membranes were incubated with primary antibodies: anti-HA 3F10 (Rat, 1:2500), anti-Tubulin (polyclonal rabbit anti β Tubulin H-235 from Santa Cruz Biotechnology, 1:2500) and Histone-3 (polyclonal rabbit anti H3 H-0164 from Merk, 1:2500). After washing, membranes were incubated with IRDye® 800CW (LI-COR Biosciences) secondary antibodies. Bound antibody was detected an Odyssey imaging system (LI-COR Biosciences).
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8

Western Blot Analysis of Protein Samples

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Protein samples were separated on 12% SDS-polyacrylamide gels and transferred to PVDF membranes.
Membranes were incubated with primary antibodies: anti-HA 3F10 (Rat, 1:2500), anti-Tubulin (polyclonal rabbit anti βtubulin H-235 from Santa Cruz Biotechnology, 1:2500) and Histone-3 (polyclonal rabbit anti H3 H-0164 from Merk, 1:2500). After washing, membranes were incubated with IRDye® 800CW (LI-COR Biosciences) secondary antibodies. Bound antibody was detected an Odyssey imaging system (LI-COR Biosciences).
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9

Protein Expression Analysis of Breast Cancer Cells

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Proteins from MCF-7, SKBR-3 cells and animal breast tissues were prepared using RIPA buffer containing protease inhibitor cocktail (Sigma, St. Louis, MO) and resolved on 10% SDS- polyacrylamide gels following standard protocols (Amersham BioSciences, Piscataway, NJ). Membrane were blotted with STARD10, ERBB2, ERK, phospho-ERK, c-MYC, p65, c-JUN, c-FOS (Proteintech, Rosemont, IL), control β-actin and Histone 3 (Sigma, St. Louis, MO) antibodies. Membranes were developed by chemiluminescence ECL detection system (Amersham BioSciences, Pittsburgh, PA) and blots were quantified using the Quantity OneTM densitometry program (Bio-Rad laboratories, Hercules, CA).
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10

Western Blot Analysis of Protein Expression

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Cell monolayers were lysed in Laemmli´s sample buffer (62.5 mM Tris-HCl [pH 6.8], 2% sodium dodecyl sulfate [SDS], 0.01% bromophenol blue, 10% glycerol and 5% β-mercaptoethanol). Protein samples were subjected to 12% SDS-polyacrylamide gel electrophoresis (PAGE) and transferred to nitrocellulose membranes (BioRad). Membranes were blocked for 30 min at room temperature in Tris-buffered saline supplemented with 0.05% Tween 20 (TBS-T) containing 5% non-fat dry milk, and later incubated with primary antibodies diluted in the same buffer at 4 °C overnight. Antibodies used in this study were β-actin (Santa Cruz Biotechnology SC-47778), c-Myc (Sigma PLA0001 or Roche 11667149001), Histone 3 (Sigma H0164), and Flag (Sigma B3111). Then, membranes were washed with TBS-T and incubated with goat anti-mouse IgG-peroxidase conjugate (Sigma DC02L) for 1 h at room temperature and washed again. All antibodies were used at a 1:10,000 dilution in TBS-T with 5% non-fat dry milk. Detection of immunoreactive proteins was carried out using the enhanced chemiluminescence (ECL) reaction (SuperSignal ThermoScientific) and detected by the ChemiDoc Touch Imaging System (BioRad).
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