Genome-wide DNA binding pattern of the homeodomain transcription factor Sine oculis (So) in the developing eye of Drosophila melanogaster.

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Among these is the homeobox gene sine oculis (so), which encodes a homeodomain transcription factor (TF) that is both necessary for eye development and sufficient to reprogram a subset of cells outside the normal eye field toward an eye fate. We have performed a genome-wide analysis of So binding to DNA prepared from developing Drosophila eye tissue in order to identify candidate direct targets of So-mediated transcriptional regulation, as described in our recent article [1]. The data are available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE52943. Here we describe the methods, data analysis, and quality control of our So ChIP-seq dataset.", "claims": [{"id": "claim-method", "statement": "Peaks were called from the mapped reads using Model-based Analysis of ChIP-Seq (MACS) [9]. The data are available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE52943.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25126519", "locator": "sections[6] \"Data analysis\" paragraph 3", "quote": "Peaks were called from the mapped reads using Model-based Analysis of ChIP-Seq (MACS) [9]."}, {"asset": "source:pmid:25126519", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data are available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE52943."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data are available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE52943.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25126519", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data are available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE52943."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study called ChIP-seq peaks using Model-based Analysis of ChIP-Seq (MACS) and obtained 7,566 peaks; the source data are available through NCBI Gene Expression Omnibus (GEO) under accession GSE52943 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52943.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25126519", "locator": "sections[6] \"Data analysis\" paragraph 3", "quote": "Peaks were called from the mapped reads using Model-based Analysis of ChIP-Seq (MACS) [9]."}, {"asset": "source:pmid:25126519", "locator": "sections[6] \"Data analysis\" paragraph 3", "quote": "A total of 7566 peaks were then obtained and annotated using an in-house bioinformatics tool (a Perl script, available upon request)."}, {"asset": "source:pmid:25126519", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data are available from NCBI Gene Expression Omnibus (GEO) with the accession number GSE52943."}, {"asset": "source:pmid:25126519", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data are available from the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52943."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study called ChIP-seq peaks using Model-based Analysis of ChIP-Seq (MACS) and obtained 7,566 peaks; the source data are available through NCBI Gene Expression Omnibus (GEO) under accession GSE52943 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE52943.", "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:25126519"], "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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