Genomic-wide transcriptional profiling in primary myoblasts reveals Runx1-regulated genes in muscle regeneration.

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We have recently showed that following myopathic damage the level of the Runx1 transcription factor (TF) is elevated and that during muscle regeneration this TF regulates the balance between myoblast proliferation and differentiation (Umansky et al.). We employed Runx1-dependent gene expression, Chromatin Immunoprecipitation sequencing (ChIP-seq), Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) and histone H3K4me1/H3K27ac modification analyses to identify a subset of Runx1-regulated genes that are co-occupied by the TFs MyoD and c-Jun and are involved in muscle regeneration (Umansky et al.). The data is available at the GEO database under the superseries accession number GSE56131.", "claims": [{"id": "claim-method", "statement": "The GSEA software [11] was used to perform gene set enrichment analysis on groups of genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697350", "locator": "sections[9] \"Functional analysis\" paragraph 2", "quote": "The GSEA software [11] was used to perform gene set enrichment analysis on groups of genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data is available at the GEO database under:\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56131.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26697350", "locator": "sections[2] \"Direct link to deposited data\" paragraphs 1-3", "quote": "The data is available at the GEO database under:\nhttp://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56131."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GSEA analysis, the study identified a subset of Runx1-regulated genes participating in muscle regeneration, with the source data deposited in GEO under accession GSE56131.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26697350", "locator": "sections[10] \"Results & discussion\" paragraph 2", "quote": "Using in vivo loss- and gain-of-function models and genome-wide transcriptional analyses we identify a subset of Runx1-regulateed genes that participate in muscle regeneration."}, {"asset": "source:pmid:26697350", "locator": "sections[10] \"Results & discussion\" paragraph 3", "quote": "GSEA analysis of genes bound by all three TFs in comparison to Runx1-responsive genes in proliferating PMs (A) or gene expression data of WT myoblasts vs. differentiated myotubes (B)."}, {"asset": "source:pmid:26697350", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data is available at the GEO database under the superseries accession number GSE56131."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GSEA analysis, the study identified a subset of Runx1-regulated genes participating in muscle regeneration, with the source data deposited in GEO under accession GSE56131.", "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:26697350"], "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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