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Comprehensive Protein Analysis Techniques

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Western blot analysis and immunohistochemical (fluorescence) staining were conducted as previously described.14 (link), 15 (link) The primary antibodies used in this study were actin monoclonal antibody (1:5000, Merck, Darmstadt, Germany), E2F1 antibody (1:1000, Cell Signaling Technology, Beverly MA, USA), GFP monoclonal antibody (1:200, Upstate, Lake Placid, NY, USA), FITC-conjugated anti-rabbit, rhodamine-conjugated anti-mouse, alkaline phosphatase–conjugated anti-rabbit antibody (1:500, Jackson ImmunoResearch Laboratories, West Grove, PA, USA), SPZ1, TWIST1, AKT, Ki67, HIF-1, Snail, Slug, Wnt5a, ZEB1, BMI1, fibronectin, E-cadherin rabbit polyclonal antibody (1:1000; GeneTex, Irvine, CA, USA). ERK1/2, PI3K monoclonal antibodies (Santa Cruz Biotechnology, Dallas, TX, USA). CD133, CD44, N-cadherin, vimentin rabbit polyclonal antibody (1:500, Abcam, Cambridge, MA, USA) All of the experiments were repeated at least three times.
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2

Comprehensive Histone and EMT Marker Analysis

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Primary antibodies for H3K4me3 (GTX128954), H3K9me3 (GTX121677), H3K27me3 (GTX121184), H3K36me3 (GTX54109), H3K79me3 (GTX54111), histone H3 (GTX122148), MMP2 (GTX104577), MMP3 (GTX100723), MMP9 (GTX100458), N-cadherin (GTX101141), E-cadherin (GTX100433), vimentin (GTX100619), Snail (GTX100754), TWIST-1 (GTX60776), Nanog (GTX100863), OCT4 (GTX101497), SOX2 (GTX101507), ABCB1 (GTX108354), ABCG2 (GTX100437) and ABCC1 (GTX88673) were purchased from GeneTex International Corporation (Hsinchu City, Taiwan). Anti-mouse and anti-rabbit IgG-conjugated horseradish peroxidase and rabbit polyclonal antibodies speci c for β-actin (Sigma-Aldrich, Merck KGaA, Darmstadt, Germany; cat. no. SI-A5441; 1:10,000) were used in this study. All other chemicals were purchased from Sigma-Aldrich (Merck KGaA, Darmstadt, Germany).
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Protein Expression Profiling Protocol

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Protein expression was measured as previously described [29 (link)], using Western blotting with antibodies (Abs) to anti-EIF2C2/AGO2 mouse monoclonal antibody (RN003M, MBL International, Nagoya, Japan), PIK3C3 (#4263; Cell Signaling Technology, Beverly, MA, USA), LC3 (PM036; MBL, Nagoya, Japan), P62 (PM045; MBL), Twist1 (GTX60776; GeneTex, Irvine, CA, USA), Snail (#3879; Cell Signaling Technology), ATG5 (#2630; Cell Signaling Technology), N-cadherin(610,920, BD Transduction Labs, San Diego, CA, USA), E-cadherin (GTX100443; GeneTex), Vimentin (GTX100619; Gentex), Fibronectin (GTX112794; GeneTex) and, β-actin (A5441; Sigma-Aldrich, St. Louis, MO, USA). Full blots were provided in the supplementary information (Supplementary Fig. S6).
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Comprehensive Antibody Staining Protocol

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Western blotting and immunohistochemical (fluorescence) staining were performed as described previously.[10, 29] The primary antibodies used in this study were PIINP and Actin polyclonal antibodies (1:5000 dilution; Sigma‐Aldrich), GFP monoclonal antibodies (1:500 dilution; Upstate, NY), FITC‐conjugated anti‐rabbit IgG, rhodamine‐conjugated antimouse IgG, and alkaline phosphatase‐conjugated anti‐rabbit IgG antibody (1:500 dilution; Jackson ImmunoResearch Laboratories), and CYP1B1 rabbit polyclonal antibody (1:200 dilution; Santa Cruz Biotechnology). The AHR goat polyclonal antibody (1:200 dilution; Santa Cruz Biotechnology). The Core protein, ISX, IDO1, TDO2, CD86, PD‐L1, N‐cadherin, E‐cadherin, Fibronectin, Vimentin, BMI1, CD133, TWIST1, Snail1, Slug, and ZEB1 (1:500 dilution) primary antibody was obtained from GeneTex International Corp. The Onecut1, GADD45G, PDGFA, SOX13, FOCX1, and LPIN1(1:500 dilution) primary antibody was obtained from Elabscience. All of the experiments were repeated at least 3 times.
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