Aristolochic acids - Induced transcriptomic responses in rat renal proximal tubule cells in vitro.

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However, AAs have recently been discovered to be highly nephrotoxic and induced urothelial cancer in humans and malignant tumors in the kidney and urinary tract of rodents. In this study, we exposed rat renal proximal tubule cells in vitro to a sub-cytotoxic level of AAs at three different time points (6 h, 24 h and 72 h). We then analyzed the gene expression profile after the compound exposure. Functional analysis with Ingenuity Pathways Analysis and DAVID tools revealed that at the late time point (72 h) there are many significantly altered genes involved in cancer-related pathways such as p53 signaling. MIAMI-compliant microarray data are deposited in the NCBI GEO database under accession number GSE68687 and can be found at: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68687.", "claims": [{"id": "claim-method", "statement": "To identify the differentially expressed (DE) probe sets, two sampled t-test (unpaired t-test) with a P-value < 0.05 and Benjamini–Hochberg correction for multiple testing correction and a fold cut off of 2 was used.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484264", "locator": "sections[13] \"Microarray analysis\" paragraph 2", "quote": "To identify the differentially expressed (DE) probe sets, two sampled t-test (unpaired t-test) with a P-value < 0.05 and Benjamini–Hochberg correction for multiple testing correction and a fold cut off of 2 was used."}], "state": "complete"}, {"id": "claim-data-access", "statement": "MIAMI-compliant microarray data were deposited in the NCBI GEO database under accession number GSE68687; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68687.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484264", "locator": "sections[15] \"Data deposition\" paragraph 2", "quote": "MIAMI-compliant microarray data were deposited in the NCBI GEO database under accession number GSE68687; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68687."}], "state": "complete"}, {"id": "claim-target-result", "statement": "No genes were differentially expressed after 6 h and 24 h exposure to AAs, whereas 1,204 genes were differentially expressed after 72 h; differential expression was identified using an unpaired two-sample t-test with P < 0.05, Benjamini–Hochberg correction, and a fold cutoff of 2, and the source data are available through NCBI GEO under accession GSE68687 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68687.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "To identify the differentially expressed (DE) probe sets, two sampled t-test (unpaired t-test) with a P-value < 0.05 and Benjamini–Hochberg correction for multiple testing correction and a fold cut off of 2 was used."}, "evidence": [{"asset": "source:pmid:26484264", "locator": "sections[17] \"Gene expression profile induced after aristolochic acids exposure\" paragraph 2", "quote": "No genes were differentially expressed after 6 h and 24 h exposure to AAs, however at 72 h, 1204 genes were found to be differentially expressed."}, {"asset": "source:pmid:26484264", "locator": "sections[13] \"Microarray analysis\" paragraph 2", "quote": "To identify the differentially expressed (DE) probe sets, two sampled t-test (unpaired t-test) with a P-value < 0.05 and Benjamini–Hochberg correction for multiple testing correction and a fold cut off of 2 was used."}, {"asset": "source:pmid:26484264", "locator": "sections[15] \"Data deposition\" paragraph 2", "quote": "MIAMI-compliant microarray data were deposited in the NCBI GEO database under accession number GSE68687; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68687."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "No genes were differentially expressed after 6 h and 24 h exposure to AAs, whereas 1,204 genes were differentially expressed after 72 h; differential expression was identified using an unpaired two-sample t-test with P < 0.05, Benjamini–Hochberg correction, and a fold cutoff of 2, and the source data are available through NCBI GEO under accession GSE68687 at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68687.", "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:26484264"], "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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