Genome-wide transcriptomic alterations induced by ethanol treatment in human dental pulp stem cells (DPSCs).

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The utility of DPSC has been explored in odontogenic differentiation for tooth regeneration. Alcohol abuse appears to lead to periodontal disease, tooth decay and mouth sores that are potentially precancerous. Persons who abuse alcohol are at high risk of having seriously deteriorated teeth, gums and compromised oral health in general. It is currently unknown if alcohol exposure has any impact on adult stem cell maintenance, stem cell fate determination and plasticity, and stem cell niche environment. Here we provide detailed experimental methods, analysis and information associated with our data deposited into Gene Expression Omnibus (GEO) under GSE57255. Our data provide transcriptomic changes that are occurring by EtOH treatment of DPSCs at 24-hour and 48-hour time point.", "claims": [{"id": "claim-method", "statement": "In addition to the linear model, we performed a regression spline analysis with moderated F-test to detect the probes differentially expressed over time with increasing dose, with the assumption that expression changes smoothly along with the increasing of the dose rather than making discrete jumps from one dose to another.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25045622", "locator": "sections[7] \"Data analysis\" paragraph 6", "quote": "In addition to the linear model, we performed a regression spline analysis with moderated F-test to detect the probes differentially expressed over time with increasing dose, with the assumption that expression changes smoothly along with the increasing of the dose rather than making discrete jumps from one dose to another."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Here we provide detailed experimental methods, analysis and information associated with our data deposited into Gene Expression Omnibus (GEO) under GSE57255.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25045622", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide detailed experimental methods, analysis and information associated with our data deposited into Gene Expression Omnibus (GEO) under GSE57255."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper analyzed ethanol-treated human dental pulp stem-cell transcriptomes using Robust Multi-array Average normalization, linear regression with dose-by-time interaction, and regression splines with moderated F-tests and false-discovery-rate control; the source data are deposited in GEO under GSE57255 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57255.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25045622", "locator": "sections[7] \"Data analysis\" paragraph 3", "quote": "We performed background correction (Fig. 2), quantile normalization and log transformation with Robust Multi-array Average (RMA) approach on Affymetrix gene expression data using “Affy” R package (Fig. 3) [2]."}, {"asset": "source:pmid:25045622", "locator": "sections[7] \"Data analysis\" paragraph 6", "quote": "We constructed linear regression models to evaluate the effect of dose and time on gene expression (Fig. 5)."}, {"asset": "source:pmid:25045622", "locator": "sections[7] \"Data analysis\" paragraph 6", "quote": "In addition to the linear model, we performed a regression spline analysis with moderated F-test to detect the probes differentially expressed over time with increasing dose, with the assumption that expression changes smoothly along with the increasing of the dose rather than making discrete jumps from one dose to another. “Limma” R packages were used for this analysis."}, {"asset": "source:pmid:25045622", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here we provide detailed experimental methods, analysis and information associated with our data deposited into Gene Expression Omnibus (GEO) under GSE57255."}, {"asset": "source:pmid:25045622", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57255"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper analyzed ethanol-treated human dental pulp stem-cell transcriptomes using Robust Multi-array Average normalization, linear regression with dose-by-time interaction, and regression splines with moderated F-tests and false-discovery-rate control; the source data are deposited in GEO under GSE57255 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57255.", "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:25045622"], "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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