Genome-wide redistribution of BRD4 binding sites in transformation resistant cells.

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We have recently reported that HGPS cells are refractory to experimental oncogenic transformation and we identified the bromodomain-containing 4 protein (BRD4) as a mediator of the transformation resistance. ChIP-sequencing experiments revealed distinct genome-wide binding patterns for BRD4 in HGPS cells when compared to control wild type cells. Here we provide a detailed description of the ChIP-seq dataset (NCBI GEO accession number GSE61325), the specific and common BRD4 binding sites between HGPS and control cells, and the data analysis procedure associated with the publication by Fernandez et al., 2014 in Cell Reports 9, 248-260 [1].", "claims": [{"id": "claim-method", "statement": "Statistically significant peaks were detected using 1% FDR as the cutoff.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25478319", "locator": "sections[6] \"ChIP-seq data analysis\" paragraph 2", "quote": "Statistically significant peaks were detected using 1% FDR as the cutoff."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw reads files in fastq format were deposited to the SRA database at NCBI (Table 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25478319", "locator": "sections[5] \"ChIP-sequencing\" paragraph 3", "quote": "Raw reads files in fastq format were deposited to the SRA database at NCBI (Table 1)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used SICER peak calling with a 1% FDR cutoff to identify distinct genome-wide BRD4 binding patterns in HGPS versus control cells, with the source data available through GEO accession GSE61325.", "kind": "quantitative", "target": {"value": 1.0, "unit": "per cent", "tolerance": null, "source": "Statistically significant peaks were detected using 1% FDR as the cutoff."}, "evidence": [{"asset": "source:pmid:25478319", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "ChIP-sequencing experiments revealed distinct genome-wide binding patterns for BRD4 in HGPS cells when compared to control wild type cells."}, {"asset": "source:pmid:25478319", "locator": "sections[6] \"ChIP-seq data analysis\" paragraph 2", "quote": "Given the reported binding nature of BRD4 [9], 200 bp window size and 400 bp gap size were chosen in the peak calling step using SICER."}, {"asset": "source:pmid:25478319", "locator": "sections[6] \"ChIP-seq data analysis\" paragraph 2", "quote": "Statistically significant peaks were detected using 1% FDR as the cutoff."}, {"asset": "source:pmid:25478319", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide a detailed description of the ChIP-seq dataset (NCBI GEO accession number GSE61325)"}, {"asset": "source:pmid:25478319", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61325."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used SICER peak calling with a 1% FDR cutoff to identify distinct genome-wide BRD4 binding patterns in HGPS versus control cells, with the source data available through GEO accession GSE61325.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:25478319"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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