Microarray dataset of transient and permanent DNA methylation changes in HeLa cells undergoing inorganic arsenic-mediated epithelial-to-mesenchymal transition.

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Inorganic arsenic is a known carcinogen, though not mutagenic. Several mechanisms have been proposed as to how inorganic arsenic drives carcinogenesis such as regulation of the cell׳s redox potential and/or epigenetics. In fact, there are gene specific studies and limited genome-wide studies that have implicated epigenetic factors such as DNA methylation in inorganic arsenic-mediated epithelial-to-mesenchymal transition (EMT). However, genome-wide studies about the impact of 1) chronic, low-dose inorganic arsenic exposure on DNA methylation patterns during inorganic arsenic-induced epithelial-to-mesenchymal transition, and 2) the removal inorganic arsenic (reversal) on DNA methylation patterns, is lacking. For this dataset, two replicates were performed with each of the samples - non-treated, inorganic arsenic-treated, and reverse-treated cells. We provide normalized and processed data, and log2 fold change in DNA methylation. The raw microarray data are available through NCBI GEO, accession number GSE95232 and a related research paper has been accepted for published in Toxicology and Applied Pharmacology (Eckstein et al., 2017) [1].", "claims": [{"id": "claim-method", "statement": "Gene ontology analysis of the differentially methylated genes revealed that many of the genes had oncogenic signatures according to the Gene Set Enrichment Analysis (Supplemental Tables 1–3).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28589171", "locator": "sections[3] \"Data\" paragraph 2", "quote": "Gene ontology analysis of the differentially methylated genes revealed that many of the genes had oncogenic signatures according to the Gene Set Enrichment Analysis (Supplemental Tables 1–3)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw microarray data are available through NCBI GEO, accession number GSE95232 and a related research paper has been accepted for published in Toxicology and Applied Pharmacology (Eckstein et al., 2017) [1].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28589171", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw microarray data are available through NCBI GEO, accession number GSE95232 and a related research paper has been accepted for published in Toxicology and Applied Pharmacology (Eckstein et al., 2017) [1]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study reports changing DNA methylation profiles in HeLa cells during chronic low-dose sodium arsenite exposure and after removal of inorganic arsenic.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28589171", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The novel dataset presented here represents the results of the changing pattern of DNA methylation profiles in HeLa cells exposed to chronic low dose (0.5 µM) sodium arsenite, resulting in epithelial-to-mesenchymal transition, as well as DNA methylation patterns in cells where inorganic arsenic has been removed."}, {"asset": "source:pmid:28589171", "locator": "sections[7] \"Data analyses\" paragraph 2", "quote": "For statistical analysis, beta values were calculated."}, {"asset": "source:pmid:28589171", "locator": "sections[7] \"Data analyses\" paragraph 2", "quote": "The Pearson correlation coefficients (PCCs) were >0.99 for all the replicates, confirming a good level of reproducibility for the chip process and indicating that the observed differential methylation between the cells (treatments) represented true biological differences."}, {"asset": "source:pmid:28589171", "locator": "sections[3] \"Data\" paragraph 2", "quote": "The Infinium Methylation EPIC BeadChip Array profile data are provided as MINiML and TXT files deposited into NCBI GEO, accession number GSE95232."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study reports changing DNA methylation profiles in HeLa cells during chronic low-dose sodium arsenite exposure and after removal of inorganic arsenic.", "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:28589171"], "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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