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7 protocols using jq1 hy 13030

1

Pancreatic Cancer Cell Line Cultivation

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Panc1 (CRL-1469), MiaPaCa2 (CRL-1420), and Su86 (CRL-1837; SU.86.86) pancreatic cancer cell lines were purchased from the American Type Culture Collection (Manassas, VA, USA). All cells were cultured under the recommended conditions. All cell lines used were tested for mycoplasma using MycoAlertTM PLUS Mycoplasma Detection Kit (Lonza, Walkersville, MD, USA), and the results were negative. Gemcitabine hydrochloride (G-4177, LC Laboratories, Woburn, MA, USA) was dissolved in sterile phosphate-buffered saline or 0.9% saline solution for in vitro and in vivo experiments, respectively. JQ1 (HY-13030, MedChem Express, Monmouth Junction, NJ, USA) and I-BET762 (MedChem Express) were dissolved in DMSO. DMSO concentration was <0.1% in vitro.
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2

Comprehensive Protein Detection Protocol

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For Western blotting primary antibodies against ARID1A (PSG3), ACTIN (C2), HSP90 (H-114), CMYC (N-262), BRD4 (H-250) were obtained from Santa Cruz Biotechnology; BRD2 (A302-582A) from Bethyl; ARID1B (AB57461) and Histone-H3(trimethylK27) (AB6002) from Abcam. Immunohistochemical analysis of paraffin-embedded xenograft slices were performed as described [26 (link)], using antibodies against Cleaved-Caspase3 from Cell Signaling (#9661); Ki67 from DAKO (M7240) and ARID1A from Sigma (HPA005456). iBET762 was obtained from Xcess Biosciences. JQ1 for the cell line experiments was kindly provided by the Bradner lab (Dana-Farber Cancer Institute, Boston, USA) [9 (link)] and later purchased from Axon Medchem (axon 1989); both batches had similar activity. JQ1 (HY-13030) used in the xenograft experiments was purchased from MedChem Express. Before use in animals, the in vitro activity of JQ1 (HY-13030) was compared to the activity of JQ1 obtained from Axon Medchem.
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3

Quantifying Nuclear Protein Foci in U2OS Cells

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U2OS cells were treated with
6% 1,6-hexanediol (240117, Sigma) prepared in DMEM for 1 min; JQ1
(HY-13030, MedChemExpress) was added to U2OS cells until its final
concentration reached 1.0 μM, and the cells were incubated for
12 h before immunofluorescence microscopy imaging. The immunofluorescence
microscopy experiments were performed following previously published
procedures.14 (link) Briefly, cells on the coverslip
were fixed in methanol/acetic acid (3:1, v/v) for 10 min, permeabilized
with 0.1% triton-X100/PBS for 15 min, and treated with 50 μg/mL
RNase A (EN0531, Thermo Fisher). After blocking with 2% BSA at room
temperature for 1 h, immunofluorescence microscopy experiments were
conducted using standard methods with BG4 (MABE917, Sigma-Aldrich),
anti-FLAG (14793S, Cell Signaling Technology), and anti-rabbit Alexa
594-conjugated (A11037, Invitrogen) antibodies. Nuclei were stained
with DAPI (D9542, Sigma). Finally, the coverslips were mounted with
ProLong Diamond Antifade Mountant (Invitrogen). Images were recorded
using an LSM880 confocal laser scanning microscope (Carl Zeiss) with
a 100× objective and analyzed with ZEN. The foci number per nucleus
were counted using Find maxima in ImageJ. The graphs were plotted
using GraphPad Prism8.
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4

Evaluating Selective Protein Inhibitors

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JQ1 (HY-13030), dBET6 (HY-112588), MZ1 (HY-107425), KB02-JQ1 (HY-129917), and MLN4924 (HY-70062) were obtained from MedChemExpress; MLN7243 (CT-M7243) was obtained from ChemieTek; MG132 (S2619) was obtained from Selleck Chemicals.
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5

Cell Line Culture and Plasmid Transfection

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All cell lines were purchased from the American Type Culture Collection. HCC1806 and HCC1937 were cultured in RPMI-1640 medium (Gibco, Grand Island, USA) supplemented with 10 % FBS (Gibco). All cell lines were cultured at 37 ℃ in a humidified atmosphere containing 5 % CO2. Plasmids lenti-KRAB-dCas9-blast and lentiGuide-Puro were gifts from professor Matthew Meyerson at Harvard University. JQ-1 (HY-13030) and THZ1 (HY-80013A) were purchased from MedChem Express (MCE, Monmouth Junction, USA).
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6

Antibodies and Peptides Used in Study

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The information on commercial
antibodies used in this study are listed as following: GST (Proteintech,
66001–1-Ig), His (Santa Cruz, sc-803), Flag (Sigma, F3165),
BRD4 (Bethyl Laboratories, A301–985A100), JMJD6 (Proteintech,
16476–1-AP), β-actin (Proteintech, 66009–1-Ig),
c-Myc (Santa Cruz, sc-8432), N-myc (Santa Cruz, sc-53993), and CCND1
(Proteintech, 60186–1-Ig). Peptides P1 to P5, TAT, TAT-PROTAC,
TAT-PiET, and TAT-PiET-PROTAC were synthesized by GenScript, all peptides
are >95% pure by HPLC analysis (see details in Supporting Information: Molecular formula strings). JQ1 (HY-13030), fulvestrant
(ICI) (HY-13636), MZ1 (HY-107425), and MG132 (HY-13259) were purchased
from MedChemExpress. iJMJD6 was synthesized in-house as previously
reported.6 (link)
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7

Diverse Chemical Probes for Epigenetic Targets

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JQ1 (HY-13030), dBET6 (HY-112588), MZ1 (HY-107425), KB02-JQ1 (HY-129917) and MLN4924 (HY-70062) were obtained from MedChemExpress. MLN7243 (CT-M7243) was obtained from ChemieTek. MG132 (S2619) was obtained from Selleck Chemicals. IBG1 was kindly provided by Alessio Ciulli's group. GNE11, TMX1, MMH1, MMH2, MMH1-NR, MMH2-NR and MMH2-Biotin were synthesized in-house (for synthetic chemistry methods, see Supplementary Note: Synthesis of compounds, characterization and spectra).
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