Transcriptome profiling of Musculus longissimus dorsi in two cattle breeds with different intramuscular fat deposition.

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In order to elucidate molecular pathways underlying the genetic variation in this trait we compared transcriptomes of Musculus longissimus dorsi (MLD) in steers of Japanese Black and Holstein Friesian cattle breeds fed a high energy diet typically applied in Japan to achieve maximum IMF content. We identified a total of 569 differentially expressed genes (DEGs) with the majority (433) up-regulated in Japanese Black cattle. This breed is characterized by an extreme capacity for IMF deposition. Subsequent Ingenuity Pathway Analysis (IPA) revealed a gene network linking parameters of cell morphology and maintenance with lipid metabolism. The data from this study were deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE75348. We provide here a dataset which is of potential value to dissect molecular pathways influencing differences in fat deposition under high-energy nutrition.", "claims": [{"id": "claim-method", "statement": "Statistical analysis was performed by JMP GENOMICS 6 (SAS Institute, Cary, USA) which includes a logarithmic scaling of expression values and Student's test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981380", "locator": "sections[7] \"Bovine microarray and data analysis\" paragraph 2", "quote": "Statistical analysis was performed by JMP GENOMICS 6 (SAS Institute, Cary, USA) which includes a logarithmic scaling of expression values and Student's test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data from this study were deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE75348.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981380", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data from this study were deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE75348."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 569 differentially expressed genes in MLD, and the source data are accessible through GEO Series accession number GSE75348.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981380", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified a total of 569 differentially expressed genes (DEGs) with the majority (433) up-regulated in Japanese Black cattle."}, {"asset": "source:pmid:26981380", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data from this study were deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE75348."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 569 differentially expressed genes in MLD, and the source data are accessible through GEO Series accession number GSE75348.", "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:26981380"], "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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