Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro.

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We have previously shown that data from a genome wide binding assay combined with transcriptional profiling is an insightful means to divulge the mechanisms directing cell type specification and the generation of tissues and subsequent organs [1]. Our earlier work identified the role of the DNA-binding homeodomain containing protein Bapx1/Nkx3.2 in midgestation murine embryos. Microarray analysis of EGFP-tagged cells (both wildtype and null) was integrated using ChIP-Seq analysis of Bapx1/Nkx3.2 and Sox9 DNA-binding proteins in living tissue.", "claims": [{"id": "claim-method", "statement": "Gene enrichment test for regions bound by Sox9 and Bapx1, we submitted the analyzed ChIP-Seq data as bed format to Genomic Regions Enrichment of Annotations Tool (GREAT) [15] version 1.8 with the following parameters, species assembly-mm9 and Association rule-Single nearest gene: 100,000 bp maximum extension, curated regulatory domains included.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27672560", "locator": "sections[6] \"Chromatin immunoprecipitation and DNA-binding motif analysis\" paragraph 2", "quote": "Gene enrichment test for regions bound by Sox9 and Bapx1, we submitted the analyzed ChIP-Seq data as bed format to Genomic Regions Enrichment of Annotations Tool (GREAT) [15] version 1.8 with the following parameters, species assembly-mm9 and Association rule-Single nearest gene: 100,000 bp maximum extension, curated regulatory domains included."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Deposited data can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36672", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27672560", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36672"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using MACS for peak calling, the study detected 2815 Bapx1/Nkx3.2 peaks and 3722 Sox9 peaks, with the data deposited in GEO under accession number GSE36672.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27672560", "locator": "sections[6] \"Chromatin immunoprecipitation and DNA-binding motif analysis\" paragraph 2", "quote": "The peak calling algorithm MACS was used to match unique reads with 2 or less mismatches, with default settings as previously described [12]."}, {"asset": "source:pmid:27672560", "locator": "sections[6] \"Chromatin immunoprecipitation and DNA-binding motif analysis\" paragraph 2", "quote": "2815 Bapx1/Nkx3.2 peaks were detected at the TSS (540)."}, {"asset": "source:pmid:27672560", "locator": "sections[6] \"Chromatin immunoprecipitation and DNA-binding motif analysis\" paragraph 2", "quote": "Many peaks were identified for Sox9 (3722)."}, {"asset": "source:pmid:27672560", "locator": "sections[6] \"Chromatin immunoprecipitation and DNA-binding motif analysis\" paragraph 2", "quote": "All data was deposited in Gene Expression Omnibus (GEO) under accession number GSE36672."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using MACS for peak calling, the study detected 2815 Bapx1/Nkx3.2 peaks and 3722 Sox9 peaks, with the data deposited in GEO under accession number GSE36672.", "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:27672560"], "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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