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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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Cardiac Protein Profiling and Western Blotting

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Whole-cell protein extracts were prepared by homogenizing cardiac tissue in RIPA Buffer (Sigma), supplemented with protease and phosphatase inhibitors (Roche Inc. Basel, Switzerland). Nuclear extracts were obtained by using the Subcellular Protein Fractionation Kit for Tissues (Thermo Scientific). Electrophoresis was performed on 3–8% gradient Nu-Page Tris-Acetate or 10% Nu-Page Bis-Tris gels and transferred to 0.2 μm Sequi-Blot PVDF membranes (Bio-Rad). The membranes were blotted with total Creb1 (Cell Signaling, Danvers, MA, USA), PKG1 (Cell Signaling), total OXPHOS (Abcam, Cambridge, UK), PGC1α (Abcam), TBP, Lamin B1, and GAPDH (Cell Signaling) antibodies. Densitometric analysis of Western blots was performed using Adobe Photoshop (Adobe Systems, San Jose, CA, USA). For representative individual gel/blots, the reference proteins (laminB1 and TBP) are shown immediately below the proteins of interest.
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Quantitative Immunoblotting Analysis of Mitochondrial Proteins

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Immunoblotting was performed as described previously [4 (link)]. Protein concentrations in mitochondria and homogenates were determined using a Bradford assay kit (Bio-Rad, Hercules, CA, USA). Equal amounts of mitochondrial and homogenate proteins from the different experimental groups were resolved on 10% SDS-PAGE and transferred onto Amersham Hybond ECL nitrocellulose membranes (GE Healthcare Bio-Sciences Corp., Pittsburgh, PA). Membranes were blocked with 5% BSA in TBS. The antibodies used in this study were against total forms of PKCɛ (1:1000), PKCδ (1:200), AT1-R (1:200), AT2-R (1:200) (Santa Cruz Biotechnology, Santa Cruz, CA), Akt (1:1000), ERK1/2 (1:1000), JNK (1:1000), p38 (1:1000), PKG-1 (1:1000), VDAC (1:1000) (Cell Signaling Technology, Danvers, MA), and GAPDH (1:10000) (Sigma-Aldrich, MO, USA). The signals were visualized by Odyssey CLx Quantitative Fluorescent Imaging System with the secondary infrared antibodies IRDye 800CW goat anti-rabbit (1:25000) and 800CW donkey anti-goat (1:25000). Results were analyzed with Image Studio Lite Software (LI-COR Biotechnology, Lincoln, NE).
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Protein Expression in H295R Cells

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H295R cells (ATCC, Manassas, VA) were cultured and maintained with DMEM:F12 medium supplemented with ITS Premix (Corning, NY), 2.5% Nu-serum, 100 U/mL penicillin and streptomycin. For western blotting analysis, cells lysates were collected with NP-40 containing protease inhibitors. Primary antibodies recognizing pGC-A (R&D systems, Minneapolis, MN), NPRC (Abcam, Waltham, MA), PDE2 (FabGennix, Frisco, TX), PKG I (Cell Signaling, Danvers, MA), GAPDH (Cell Signaling) and anti-IgG secondary antibodies (Santa Cruz Biotechnology, Dallas, TX) were used.
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5

Comprehensive Evaluation of HCC Cell Lines

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All the human HCC cell lines including BEL-7402 and Huh7 were obtained from Cell Bank of Type Culture Collection of Chinese Academy of Sciences (Shanghai, China). Cells are cultured in Dulbecco's modified Eagle medium (Sigma-Aldrich, St Louis, MO, USA) replenished with 10% fetal bovine serum (Gibco, Grand Island, NY, USA) at 37 °C in a humidified incubator containing 5% CO2. Antibodies against MMP28, Notch3, Flag-tag and GAPDH were purchased from Proteintech (Chicago, IN, USA). Antibodies against ZEB-1, ZEB-2, Snail, E-cadherin, N-cadherin, Vimentin, β-catenin, Notch4, Akt, phospho-Akt (Ser473/Thr308), PKG-I, VASP and phospho-VASP (Ser239) were purchased from Cell Signaling Technology (Beverly, MA, USA).
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