Microarray-based analysis of plasma cirDNA epigenetic modification profiling in xenografted mice exposed to intermittent hypoxia.

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IH has been proposed as a major determinant of oncogenetically-related processes such as tumor growth, invasion and metastasis. During the growth and expansion of tumors, fragmented DNA is released into the bloodstream and enters the circulation. Circulating tumor DNA (cirDNA) conserves the genetic and epigenetic profiles from the tumor of origin and can be isolated from the plasma fraction. Here we report a microarray-based epigenetic profiling of cirDNA isolated from blood samples of mice engrafted with TC1 epithelial lung cancer cells and controls, which were exposed to IH during sleep (XenoIH group, n = 3) or control conditions, (i.e., room air (RA); XenoRA group, n = 3) conditions. To prepare the targets for microarray hybridization, we applied a previously developed method that enriches the modified fraction of the cirDNA without amplification of genomic DNA. Regions of differential cirDNA modification between the two groups were identified by hybridizing the enriched fractions for each sample to Affymetrix GeneChip Human Promoter Arrays 1.0R. Microarray raw and processed data were deposited in NCBI's Gene Expression Omnibus (GEO) database (accession number: GSE61070).", "claims": [{"id": "claim-method", "statement": "One-way ANOVA was used to detect probes showing differential cirDNA modification between the groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484214", "locator": "sections[12] \"Assessment of differential cirDNA modification\" paragraph 2", "quote": "One-way ANOVA was used to detect probes showing differential cirDNA modification between the groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray raw and processed data were deposited in NCBI's Gene Expression Omnibus (GEO) database (accession number: GSE61070).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484214", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Microarray raw and processed data were deposited in NCBI's Gene Expression Omnibus (GEO) database (accession number: GSE61070)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:26484214"], "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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