Gene expression in the mouse brain following early pregnancy exposure to ethanol.

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Behavioural and cognitive deficits reported in individuals exposed to alcohol in utero include intellectual impairment, learning and memory difficulties, diminished executive functioning, attention problems, poor motor function and hyperactivity [2]. The economic and social costs of these outcomes are substantial and profound [3], [4]. Improvement of neurobehavioural outcomes following prenatal alcohol exposure requires greater understanding of the mechanisms of alcohol-induced damage to the brain. Here we use a mouse model of relatively moderate ethanol exposure early in pregnancy and profile gene expression in the hippocampus and caudate putamen of adult male offspring. The effects of offspring sex and age on ethanol-sensitive hippocampal gene expression were also examined. All array data are available at the Gene Expression Omnibus (GEO) repository under accession number GSE87736.", "claims": [{"id": "claim-method", "statement": "Statistical analyses utilized the Mann-Whitney test (unpaired); P-value computation was set as “permutation” with a significance level of 0.05 and a fold change cut-off of 1.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27812507", "locator": "sections[6] \"Gene expression profiling on bead-based arrays and data analysis\" paragraph 3", "quote": "Statistical analyses utilized the Mann-Whitney test (unpaired); P-value computation was set as “permutation” with a significance level of 0.05 and a fold change cut-off of 1.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All array data are available at the Gene Expression Omnibus (GEO) repository under accession number GSE87736.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27812507", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All array data are available at the Gene Expression Omnibus (GEO) repository under accession number GSE87736."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using an unpaired Mann–Whitney test with a 1.5-fold-change cutoff and uncorrected P ≤ 0.05, the study identified four differentially expressed genes in the P87 male hippocampus, with follow-up qRT-PCR confirming increased Slc17a6 expression; the source array data were deposited in GEO under accession GSE87736.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27812507", "locator": "sections[7] \"Results\" paragraph 2", "quote": "Four genes were identified to be differentially expressed the adult (P87) male hippocampus in ethanol-exposed mice compared to controls (fold change > 1.5, uncorrected P ≤ 0.05)."}, {"asset": "source:pmid:27812507", "locator": "sections[7] \"Results\" paragraph 2", "quote": "After filtering, two candidate genes Slc17a6 and Tshz2 were selected for follow-up qRT-PCR experiments which confirmed ethanol-associated increased expression of Slc17a6 in the adult male hippocampus [7]."}, {"asset": "source:pmid:27812507", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All array data are available at the Gene Expression Omnibus (GEO) repository under accession number GSE87736."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using an unpaired Mann–Whitney test with a 1.5-fold-change cutoff and uncorrected P ≤ 0.05, the study identified four differentially expressed genes in the P87 male hippocampus, with follow-up qRT-PCR confirming increased Slc17a6 expression; the source array data were deposited in GEO under accession GSE87736.", "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:27812507"], "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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