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3 protocols using general tissue culture materials

1

Chromatin immunoprecipitation protocol for BRD proteins

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General tissue culture materials were obtained from VWR International. Antibodies against BRD2 (ab139690), BRD3 (ab50818), BRD4 (ab128874) and IRF1 (ab26109) antibody for chromatin immunoprecipitation (ChIP) were obtained from Abcam. Antibodies against c-MYC (5605), human PD-L1 (E1L3N clone; 13684), IRF1 (8478) and control IgG (2729) antibody for ChIP were purchased from Cell Signaling Technology. Anti-BRD4 (A301–985A) antibody for ChIP was obtained from Bethyl Laboratories. PE-conjugated human PD-L1 (MIH1 clone; 12-5983-42) antibody was from Thermo Fisher. The GAPDH (MAB374) antibody was from Millipore, and α-tubulin (sc-8035) antibody and HSP90 (sc-7940) antibody were obtained from Santa Cruz Biotechnology. Secondary anti-mouse IgG (A4416) and anti-rabbit IgG (A6667) antibodies were purchased from Sigma. The BET inhibitors JQ1 and I-BET151 were obtained from Tocris Bioscience, the BET PROTAC ARV-825 was obtained from MedChem Express, and human and mouse IFN-γ was purchased from Thermo Fisher Scientific. The siRNAs against BRD2, BRD3, BRD4, c-MYC, and IRF1 were purchased from Thermo Fisher Scientific.
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2

Comprehensive Molecular Profiling of Cellular Signaling

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General tissue culture materials were obtained from VWR International. Antibodies against eIF4E, tubulin, HSP90, ZEB1 and Dicer were obtained from Santa Cruz, while antibodies against p-eIF4E, MNK1, p-MNK1 and Drosha were purchased from Cell Signaling. Anti-GAPDH antibody was from Millipore, anti-E-cadherin antibody was obtained from BD Bioscience, while anti-vimentin antibody was from Abcam. Secondary antibodies were purchased from Sigma. CGP57380 was obtained from Santa Cruz. siRNAs against MNK1 and MNK2 were purchased from Dharmacon, ZEB1 siRNA was obtained from Life Technologies, while eIF4E and hnRNPA1 siRNAs were from Santa Cruz. Aldefluor assay kit was purchased from Stemcell Technologies.
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3

Chromatin Immunoprecipitation and Transcription Factor Regulation

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General tissue culture materials were obtained from VWR International. Antibodies against Snail and BRD4 were obtained from Abcam. Antibodies against c-MYC, p21 and FOSL1 were purchased from Cell Signaling, HMGA2 antibody was from Biocheck Inc, while vimentin antibody was from Abcam. Alpha-tubulin antibody was obtained from Santa Cruz, while E-cadherin antibody was from BD Bioscience. Secondary antibodies were purchased from Sigma. The EZ-Chip and EZ-Zyme Chromatin Prep kits were from Millipore. The anti-BRD4 antibody for ChIP assay was purchased from Bethyl Laboratories, while the anti-RNA polymerase II antibody and control IgG antibody were from Millipore. BET inhibitor JQ1 was obtained from BPS Bioscience, while I-BET151 was acquired from Tocris Bioscience. BRD4, c-MYC, and FOSL1 siRNAs were purchased from Life Technologies.
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