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4 protocols using histone h3k27me3

1

Antibodies in Immunoblotting and Immunofluorescence

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The following antibodies were used at the indicated dilutions: PME‐1, Santa Cruz Biotechnology (Dallas, TX, USA) sc‐20086 (H‐226), Western blotting 1 : 1000; PME‐1, Santa Cruz Biotechnology sc‐25278 (B‐12), Immunohistochemistry 1 : 1000, Immunofluorescence 1 : 100; cleaved PARP‐1, Abcam (Cambridge, UK) ab32064 [E51], Western blotting 1 : 1000; GAPDH, HyTest 5G4‐6C5, Western blotting 1 : 5000; c‐MYC, Abcam ab32072 [Y69], Western blotting 1 : 1000; p‐Myc S62, Abcam ab78318, Western blotting 1 : 1000; AKT1/2/3, Cell Signaling Technology #9272, Western blotting 1 : 2000; p‐AKT S473, Cell Signaling Technology #4060, Western blotting 1 : 1000; Lamin‐A/C, Santa Cruz Biotechnology sc‐7292 (636), Immunofluorescence 1 : 250; Lamin‐A/C, Santa Cruz Biotechnology sc‐6215 (N‐18), Western blotting 1 : 1000; p‐Lamin‐A/C S392, Abcam ab58528, Western blotting 1 : 5000; EEA1, Santa Cruz Biotechnology sc‐137130 [G4], Immunofluorescence 1 : 100; p‐FAK Y397, Cell Signaling Technology #8556, Immunofluorescence 1 : 100; Histone H3K9me3, Cell Signaling Technology #13969 [D4W1U], Immunofluorescence 1 : 500; Histone H3K27me3, Cell Signaling Technology #9733 [C36B11], Immunofluorescence 1 : 500; PPP2R2A, Cell Signaling Technology #5689, Western blotting 1 : 1000.
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2

Comprehensive ChIP-seq and Immunoblotting Protocol

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Antibodies used for ChIP-seq were BRD4 (Bethyl, A301–985A), BRD2 (Cell signaling, 5848), BRD7 (Cell Signaling, 14910), histone H3K27ac (Abcam, ab4729), histone H3K4me3 (Abcam, ab1012), and histone H3K27me3 (Cell Signaling, 9733). Antibodies used for immunoblotting were RB (Cell Signaling, 9313), CCND1 (Cell Signaling, 2978), CDK4 (Cell Signaling, 12790), E2F1 (Cell Signaling, 3742), phospho-Rb-Ser780 (Cell Signaling, 3590), phospho-Rb-Ser807/811 (Cell Signaling, 9308). Antibodies used for Immunofluorescence were BRD4 (Bethyl, A301–985A), cleaved Caspas-3 (9664), phospho-Rb-Ser807/811 (Cell Signaling, 8516), and pSTAT3 (Cell Signaling, 9131).
The JAK2 (INC424), Bcl-2 (ABT-199, S8048), and Bcl-xl/Bcl-2 (ABT263, S1001) inhibitors were from Selleckchem. The CDK4/6 inhibitor (palbociclib, HY-50767A) was from MedChemExpress. The dBET series (dBET1 - dBET10) was synthesized by Dr. Dennis Buckley (Dana Farber Cancer Institute). JQ1 was synthesized by Dr. Jun Qi (Dana Farber Cancer Institute).
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3

Comprehensive Protein Expression Analysis

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Total cell lysates were prepared in a buffer [50 mM Tris‐HCl (pH 7.5), 150 mM NaCl, 1% IGEPAL, 0.1% SDS, and 0.5% sodium deoxycholate] supplemented with a mixture of protease and phosphatase inhibitors. Protein concentrations were measured using the bicinchoninic acid protein assay reagent kit (Pierce Chemical Co). Equal amounts (20ug) of protein lysates from various samples were used for SDS–PAGE analysis followed by immunoblotting. Antibodies to cyclin B1 (12231), cyclin A2 (4656), cyclin D3 (2936), vinculin (13901), Eg5 (14404), Histone H3 K27 Me3 (9733), Histone H2A K119 Ub1 (8240), phospho‐Histone H3 (Ser 10) (3377), DYKDDDDK (FLAG Tag) (14793), BubR1 (4116), CBX8 (14696), PARP‐1 (9542), α‐Tubulin (2144), Histone H2A (12349), phospho‐Histone H2Ax (2577) and β‐Actin (4970) were purchased from Cell Signaling Technology. Anti‐GST (Z‐5), Bub3 (H‐100), Histone H3 (FL‐136) and p55 CDC (H‐175) (Cdc20) antibody were purchased from Santa Cruz biotechnology. Antibodies to MAD2 (A300‐301A) and PTEN (A300‐700A) were obtained from Bethyl laboratories. Specific signals on immunoblots (polyvinylidene difluoride) were visualized using enhanced chemiluminescence (Super‐Signal, Pierce Chemical Co.).
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4

CENP-A Chromatin Profiling in Cell Lines

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Salt fractionation N-ChIP assays were performed in the CENP-A Flag-tagged HT1080-1b cell line (Thakur and Henikoff 2016 (link)), and CUT&RUN.Salt experiments were performed in the K562 cell line. The antibodies used were anti-CENP-A (Abcam, ab13939), anti-CENP-B (Abcam, ab25734), anti-CENP-C (Abcam, ab33034), Histone H3K27me3 (Cell Signaling Technologies, 9733), IgG (Antibodies Online, ABIN102961) and MTPOL (GeneTex, GTX105137). qPCR primers are listed in Supplemental Table 2.
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