{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Giulio Aceto"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15699"],"description":["We aim to test how SMARCA4 restoration impacts p300 occupancy distribution. To this aim we generated ChIP-seq samples in BIN-67 with or without A-485 treatment (1 μM, 24h), as a proxy for p300 acetylatransferase inhibition, and BIN-67 with inducible SMARCA4 restoration (1 μg/ml Doxycycline for 24h). We pulled down p300 and H3K27ac as a marker for p300 acetyltransferase activity on the chromatin."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - BIN-67, BIN-67 with inducible SMARCA4 restoration were cultured in Roswell Park Memorial Institute 1640 Medium (RPMI, Thermo Fisher Scientific, Cat# 11875-093; no pyruvate) with 6% tetracycline free fetal bovine serum (Wisent Inc., Cat# 081150), 1% penicillin/streptomycin (Thermo Fisher Scientific, Cat# 15140-122), and 2 mM L-glutamine (Thermo Fisher Scientific, Cat# 25030-081). Cells were maintained in a humidified 5% CO2-containing incubator at 37°C and regular Mycoplasma test was performed using Mycoalert Detection Kit (Lonza, Cat# LT07-318). Cells were fixed in complete media with 0.3% formaldehyde for 30 minutes at 4°C and then quenched by adding 0.125 mol/L glycine for 5 minutes at room temperature and 15 minutes on ice. Fixed BIN-67 or BIN-67 TP53KO cells ± restoration of SMARCA4 were pelleted and washed once with 1× PBS before snap-freezing on dry ice.","Nucleic Acid Extraction - Cells were fixed in complete media with 0.3% formaldehyde for 30 minutes at 4°C and then quenched by adding 0.125 mol/L glycine for 5 minutes at room temperature and 15 minutes on ice. Fixed BIN-67 or BIN-67 TP53KO cells ± restoration of SMARCA4 were pelleted and washed once with 1× PBS before snap-freezing on dry ice. Antibodies against H3K27ac (ab4729, Abcam), HDAC2 (ab124974, Abcam), p300 (ab14984, Abcam), HDAC1 (40967, Active Motif), p53(sc-126, Santa Cruz Biotechnology)  were used for chromatin immunoprecipitation (ChIP) experiments following a protocol with MNase. Briefly, the cell pellet was resuspended in 1 mL buffer A (25 mmol/L HEPES–NaOH, pH 7.5; 10 mmol/L KCl; 0.1% NP-40; and 1.5 mmol/L MgCl2) and homogenized. Nine volumes of buffer B (15 mmol/L HEPES–NaOH, pH 7.9; 15 mmol/L NaCl; 60 mmol/L KCl; 0.5 mmol/L phenylmethylsulfonylfluoride; and 0.32 mol/L sucrose) were added, and the mixture was centrifuged at 2,000 rpm (at 4°C for 7 minutes) to collect nuclei. The nuclei were resuspended in 1 mL buffer B and 3.3 µL of 1 mol/L CaCl2 and then prewarmed at 37°C for 15 minutes. MNase (1 µL, New England Biolabs, M0247S) was added and incubated at 37°C for 15 minutes. The reaction was quenched with 10 µmol/L EGTA on ice for 5 minutes. One volume of 2× buffer C (20 mmol/L Tris–HCl, pH 8.0; 200 mmol/L NaCl; 2 mmol/L EDTA; 1 mmol/L EGTA; 0.2% Na-deoxycholate; and 1% N-lauroylsarcosine) and Triton X-100 (final 1%) was added. Samples were then passed through a 21G needle five times and centrifuged at 13,000 g (4°C) for 15 minutes. Five micrograms of antibodies were added to the lysate for overnight incubation at 4°C. Protein G Magnetic Dynabeads (Thermo Fisher Scientific) were used for pulldown. Immunoprecipitated chromatin bound to Dynabeads was washed four times with RIPA buffer (50 mmol/L HEPES-KOH, pH 7.5; 500 mmol/L LiCl; 1 mmol/L EDTA; 1% NP-40; and 0.7% Na-deoxycholate). Chromatin was eluted from Dynabeads in 100 µL elution buffer (50 mmol/L Tris-HCl, pH 8.0; 10 mmol/L EDTA; and 1% SDS) by incubating at 65°C for 30 minutes. Immunoprecipitated samples and input were incubated overnight at 65°C to denature formaldehyde cross-linking. Samples were then treated with RNase A (Thermo Fisher Scientific), followed by proteinase K (Sigma-Aldrich).Genomic DNA was extracted using a Zymo kit(D5205, Zymo Research, Irvine, CA, USA).","Library Construction - 1ug total DNA was used for the library construction. ChIP-sequencing (ChIP-seq) libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.","Sequencing - Samples were sequenced in with an Illumina NextSeq 500 instrument."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - ChIP-seq data were mapped to the human reference genome (hg38) using Bowtie2 (v2.4.6) with default parameters. Duplicate reads were removed with SAMtools (v1.17). Peak calling was performed with MACS2 (v2.2.8). For visualization, normalized coverage tracks (.bw) were generated using deepTools (v3.5.5) with bamCoverage in RPGC mode and an effective genome size of 2,913,022,398. Coverage was calculated in 10 bp bins with reads extended to 300 bp, and normalization excluded the Epstein–Barr virus (chrEBV) sequence."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["ChIP-seq"],"species":["Homo sapiens"],"pubmed_authors":["Giulio Aceto","Sidong Huang"],"additional_accession":[]},"is_claimable":false,"name":"Assessing SMARCA4 restoration contribution to global changes in p300 occupancy in BIN-67 cells","description":"We aim to test how SMARCA4 restoration impacts p300 occupancy distribution. To this aim we generated ChIP-seq samples in BIN-67 with or without A-485 treatment (1 μM, 24h), as a proxy for p300 acetylatransferase inhibition, and BIN-67 with inducible SMARCA4 restoration (1 μg/ml Doxycycline for 24h). We pulled down p300 and H3K27ac as a marker for p300 acetyltransferase activity on the chromatin.","dates":{"release":"2026-05-05T00:00:00Z","modification":"2026-05-05T18:01:20.492Z","creation":"2025-10-09T21:35:37.292Z"},"accession":"E-MTAB-15699","cross_references":{"ENA":["ERP181298"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002692","EFO_0005518","EFO_0003816","EFO_0004184"]}}