Gene expression profile of Musculus longissimus dorsi in bulls of a Charolais × Holstein F2-cross with divergent intramuscular fat content.

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Two groups of 10 bulls were selected which differed significantly in intramuscular fat (IMF) deposition despite standardized husbandry and feeding conditions and identical sires in both groups. Consequently, genetic factors underlying the different capability of IMF deposition should be identified. A total of 32 differentially expressed genes (DEGs) were found of which 11 were up-regulated and 21 were down-regulated in the high IMF group. Ingenuity Pathway Analysis (IPA) identified a gene network comprising DEGs with functions in carbohydrate metabolism, lipid metabolism and molecular transport. The data from this study were deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE75347. We provide here a dataset which is of potential value to dissect molecular pathways influencing differences in IMF deposition in crossbred cattle with standardized genetic background.", "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 t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981388", "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 t-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 GSE75347.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981388", "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 GSE75347."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using logarithmic scaling and Student's t-test, the study identified 32 differentially expressed genes between high- and low-intramuscular-fat bulls; the source data are available through GEO Series accession GSE75347.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981388", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 32 differentially expressed genes (DEGs) were found of which 11 were up-regulated and 21 were down-regulated in the high IMF group."}, {"asset": "source:pmid:26981388", "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 GSE75347."}, {"asset": "source:pmid:26981388", "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 t-test."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using logarithmic scaling and Student's t-test, the study identified 32 differentially expressed genes between high- and low-intramuscular-fat bulls; the source data are available through GEO Series accession GSE75347.", "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:26981388"], "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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