Genome-wide p63-regulated gene expression in differentiating epidermal keratinocytes.

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To investigate this, we recently generated genome-wide profiles of gene expression, p63 binding sites and active regulatory regions with the H3K27ac histone mark (Kouwenhoven et al., 2015). We showed that only a subset of p63 binding sites are active in keratinocytes, and that differentiation-associated gene expression dynamics correlate with the activity of p63 binding sites rather than with their occurrence per se. Here we describe in detail the generation and processing of the ChIP-seq and RNA-seq datasets used in this study. These data sets are deposited in the Gene Expression Omnibus (GEO) repository under the accession number GSE59827.", "claims": [{"id": "claim-method", "statement": "Transcript quantification was performed with cufflinks and cuffdiff v2.1.1 [12], using the RefSeq transcriptome [8] which was downloaded from the UCSC genome browser website [9] in June 2013.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484246", "locator": "sections[10] \"RNA-seq data processing\" paragraph 2", "quote": "Transcript quantification was performed with cufflinks and cuffdiff v2.1.1 [12], using the RefSeq transcriptome [8] which was downloaded from the UCSC genome browser website [9] in June 2013."}], "state": "complete"}, {"id": "claim-data-access", "statement": "These data sets are deposited in the Gene Expression Omnibus (GEO) repository under the accession number GSE59827.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484246", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These data sets are deposited in the Gene Expression Omnibus (GEO) repository under the accession number GSE59827."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Only a subset of p63 binding sites are active in keratinocytes, and differentiation-associated gene expression dynamics correlate with the activity of p63 binding sites rather than with their occurrence per se.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484246", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We showed that only a subset of p63 binding sites are active in keratinocytes, and that differentiation-associated gene expression dynamics correlate with the activity of p63 binding sites rather than with their occurrence per se."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Only a subset of p63 binding sites are active in keratinocytes, and differentiation-associated gene expression dynamics correlate with the activity of p63 binding sites rather than with their occurrence per se.", "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:26484246"], "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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The", "pitation of p63 followed by deep sequencing (ChIP-seq) analysis, in order to identify the genome-w", "e of differentiation. We similarly performed ChIP-seq of the H3K27ac histone modification, which m", "easure gene activity we used two approaches: ChIP-seq of RNA polymerase II (RNAPII) in order to id"], "order_basis": "paper_text_order:727", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["eneration and processing of the ChIP-seq and RNA-seq datasets used in this study. These data sets", "ng active transcription, and RNA sequencing (RNA-seq) in order to measure steady state RNA levels", "eadily detectable by RNAPII ChIP-seq than by RNA-seq [1]. This combination of datasets allowed us", "shot from genome browser (UCSC) to visualize RNA-seq, and ChIP-seq signal at the TP63 gene locus"], "order_basis": "paper_text_order:739", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["of differentiation. This process mimics the in vivo keratinocyte differentiation process [2]. 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