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4 protocols using anti h3k27ac d5e4

1

Comprehensive Protein Expression Analysis

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Cells were lysed with RIPA lysis buffer. Anti‐ERɑ mouse (1D5, SC56833) was from Santa Cruz Biotechnology. Anti‐ERɑ rabbit (D8H8, #8644) was from Cell Signaling Technology. Anti‐RNF168 (SC‐101125) was acquired from Santa Cruz Biotechnology. Anti‐SRC1 (128E7), anti‐SRC3 (5E11) and anti‐H3K27ac (D5E4) antibodies were acquired from Cell Signaling Technology. Anti‐PolII (PLA0127) and anti‐P300 (HPA003128) were acquired from Sigma. Anti‐tubulin (T‐5168) and anti‐histone‐3 (Ab18521) were acquired from Sigma and Abcam, respectively. Anti‐actin (8H10D10) was acquired from Cell Signaling Technology.
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2

Molecular Tools for CREPT and STAT3 Studies

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Flag-CREPT, Myc-CREPT, Myc-CREPT/RPR, Myc-CREPT/CCT, Flag-STAT3, APRE (acute phase response element)-luciferase and pCDH-HA-CREPT were constructed in this laboratory. HA-p300 plasmid was a gift from Dr. Y. Eugene Chin (Institutes of Biology and Medical Sciences, Soochow University). Anti-STAT3 (c-20), anti-Myc (9E10) and anti-HA (F-7) were purchased from Santa Cruz Biotechnology (Santa Cruz). Anti-p300 (D2X6N), anti-c-MYC, anti-cyclinD1 (SP4), anti-pY705 STAT3 (D3A7), anti-pS727 STAT3, anti-acK685 STAT3, anti-Bcl-XL (54H6), anti-H3K18ac (D8Z5H) and anti-H3K27ac (D5E4) antibodies were purchased from Cell Signaling Technology. Anti-actin (AC-15) and anti-Flag (M2) antibodies were purchased from Sigma. Anti-CREPT antibody was prepared by this laboratory.50 (link) The cytokine leukaemia inhibitory factor (LIF) was purchased from Millipore (cat. #LIF1010). Short interfering RNAs (siRNAs) against CREPT or p300 were synthesised from GenePharma (SuZhou GenePharma Co. Ltd) with the oligo sequence information as shown in Table S1. The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated 9)-mediated CREPT deletion plasmids were generated based on PX458M vector with guider RNAs and the sequence information was shown in Table S1.
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3

ChIP-seq Protocol with Antibody Validation

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ChIP-seq was performed either manually on individual samples or automatically using the Bravo liquid handling platform (Agilent model 16050-102, “Bravo”) as described previously (Busby et al. 2016 (link)). In accordance with our efforts to promote reproducibility, all antibodies used were monoclonal. The following antibodies were used: anti-RNA polymerase II 8WG16 (ab817, Abcam), anti-H3K4me1 (D1A9, Cell Signaling Technology), anti-H3K4me3 (C42D8, Cell Signaling Technology), anti-H3K9ac (C5B11, Cell Signaling Technology), anti-H3K27ac (D5E4, Cell Signaling Technology), anti-H3K27me3 (C36B11, Cell Signaling Technology), anti-H3K36me3 (D5A7, Cell Signaling Technology), and anti-CTCF G.758.4 (MA5-11187, Invitrogen). The specificity of all antibodies targeting histone modifications were assessed by us (Busby et al. 2016 (link)) and others (Rothbart et al. 2015 (link)), and the array data sets are publicly available at www.histoneantibodies.com.
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4

Western Blot Antibody Detection Protocol

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The following primary antibodies were used for western blots: anti-TUBULIN, T6199 mouse (1/10,000, Sigma Aldrich, St. Louis, MO, USA); anti-Beta-ACTIN, 13854 (1/20,000 Sigma Aldrich); anti-SMARCA4 49360S (1:1000, Cell Signaling Technology); anti-EZH2 5246S (1:1000, Cell Signaling); anti-H3K27ac D5E4 (1:1000, Cell Signaling) anti-H3K27me3 07-449 (1:1000, Cell Signaling); anti-UTX (KDM6A) D3Q1I (1:1000, Cell Signaling); anti-KDM6B (JMJD3) #3457 (1:1000, Cell Signaling) for western blots or anti-KDM6B (JMJD3) ab38113 (Abcam) for immunostaining (see also Supplementary Table 1). For western blots, whole-cell lysates were collected in a buffer containing 2% SDS 50 mM Tris–HCl (pH 7.4), 10% glycerol and protease inhibitor cocktail (Roche Applied Science). Protein concentrations were determined using a Bio-Rad DC Protein Assay kit (Life Science Research). Equal amounts of lysates (20 µg) were separated by SDS–PAGE and transferred to a nitrocellulose membrane that was blocked with 5% nonfat dry milk. Membranes were incubated with the primary antibody overnight at 4 °C, then washed before incubation with species-appropriate IRDye 680CW (925-68022) or IRDye 800CW (925-32213) fluorescent secondary antibodies (1:10,000 LI-COR, NE, USA) for 1 h at room temperature. Membrane imaging was performed on the Odyssey Li-Cor CLx i software: Image Studio Lite v5.2.
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