Transcriptomic profiling comparison of YAP over-expression and conditional knockout mouse tooth germs.

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Our results showed that some Hox, Wnt and Laminin family genes had concurrent changes with YAP transcripts, indicating that the expression of these genes may be regulated by YAP. Here, we provide the detailed experimental procedure for the transcriptomic profiling results (NCBI GEO accession number GSE65524). The associated study on the regulation of Hoxa1 and Hoxc13 genes by YAP was published in Molecular Cellular Biology in 2015 [Liu et al., 2015].", "claims": [{"id": "claim-data-access", "statement": "RNA-Seq raw sequencing reads and aligned reads are available through the Gene Expression Omnibus at the accession number of GSE65524.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484260", "locator": "sections[7] \"Data analysis\" paragraph 2", "quote": "RNA-Seq raw sequencing reads and aligned reads are available through the Gene Expression Omnibus at the accession number of GSE65524."}], "state": "complete"}, {"id": "claim-target-result", "statement": "RNA-Seq comparison of Yap conditional-knockout and YAP-overexpression E14.5 mouse tooth germs, using a 1.5-fold change cutoff, identified 968 downregulated and 979 upregulated genes in Yap CKO and 1,289 downregulated and 774 upregulated genes in YAP overexpression; the source data are available through GEO accession GSE65524.", "kind": "quantitative", "target": {"value": 1.5, "unit": "fold change", "tolerance": null, "source": "In comparison with the corresponding controls at the 1.5-fold change cutoff, there were 968 down-regulated genes and 979 up-regulated genes in Yap CKO tooth germs, while there were down-regulated 1289 genes and up-regulated 774 genes in YAP over-expression tooth germs (Fig. 2)."}, "evidence": [{"asset": "source:pmid:26484260", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our results showed that some Hox, Wnt and Laminin family genes had concurrent changes with YAP transcripts, indicating that the expression of these genes may be regulated by YAP."}, {"asset": "source:pmid:26484260", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we provide the detailed experimental procedure for the transcriptomic profiling results (NCBI GEO accession number GSE65524)."}, {"asset": "source:pmid:26484260", "locator": "sections[7] \"Data analysis\" paragraph 2", "quote": "In comparison with the corresponding controls at the 1.5-fold change cutoff, there were 968 down-regulated genes and 979 up-regulated genes in Yap CKO tooth germs, while there were down-regulated 1289 genes and up-regulated 774 genes in YAP over-expression tooth germs (Fig. 2)."}, {"asset": "source:pmid:26484260", "locator": "sections[7] \"Data analysis\" paragraph 2", "quote": "RNA-Seq raw sequencing reads and aligned reads are available through the Gene Expression Omnibus at the accession number of GSE65524."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "RNA-Seq comparison of Yap conditional-knockout and YAP-overexpression E14.5 mouse tooth germs, using a 1.5-fold change cutoff, identified 968 downregulated and 979 upregulated genes in Yap CKO and 1,289 downregulated and 774 upregulated genes in YAP overexpression; the source data are available through GEO accession GSE65524.", "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:26484260"], "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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