Transcriptional profile of immediate response to ionizing radiation exposure.

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Previously proposed gene biomarkers for radiation exposure include phosphorylated H2A Histone Family, Member X (γH2AX), Tumor Protein 53 (TP53), and Cyclin-Dependent Kinase Inhibitor 1A (CDKN1A). However, transcripts of these genes may not be the most suitable biomarkers for radiation exposure due to a lack of sensitivity or specificity. As part of a larger effort to develop lab-on-a-chip methods for detecting radiation exposure events using blood samples, we designed a dose-course microarray study in order to determine coding and non-coding RNA transcripts undergoing differential expression immediately following radiation exposure. The main goal was to elicit a small set of sensitive and specific radiation exposure biomarkers at low, medium, and high levels of ionizing radiation exposure. Four separate levels of radiation were considered: 0 Gray (Gy) control; 0.3 Gy; 1.5 Gy; and 3.0 Gy with four replicates at each radiation level. This report includes raw gene expression data files from the resulting microarray experiments from all three radiation levels ranging from a lower, typical exposure than an astronaut might see (0.3 Gy) to high, potentially lethal, levels of radiation (3.0 Gy). The data described here is available in NCBI's Gene Expression Omnibus (GEO), accession GSE64375.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs), defined as Affymetrix® transcript sets, were determined using Limma [8] and a p-value cutoff of 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981369", "locator": "sections[7] \"Data acquisition\" paragraph 4", "quote": "Differentially expressed genes (DEGs), defined as Affymetrix® transcript sets, were determined using Limma [8] and a p-value cutoff of 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is available in the Gene Expression Omnibus (GEO) [1], [2] accession GSE64375 through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64375", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981369", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Data is available in the Gene Expression Omnibus (GEO) [1], [2] accession GSE64375 through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64375"}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using Limma with a p-value cutoff of 0.05, the study identified approximately 400–500 differentially expressed genes at each radiation level relative to control; the raw CEL source files are available through GEO accession GSE64375.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26981369", "locator": "sections[7] \"Data acquisition\" paragraph 4", "quote": "Differentially expressed genes (DEGs), defined as Affymetrix® transcript sets, were determined using Limma [8] and a p-value cutoff of 0.05."}, {"asset": "source:pmid:26981369", "locator": "sections[7] \"Data acquisition\" paragraph 4", "quote": "Using these levels, approximately 400–500 differentially DEGs were determined at each radiation level, relative to control (Table 3)."}, {"asset": "source:pmid:26981369", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data described here is available in NCBI's Gene Expression Omnibus (GEO), accession GSE64375."}, {"asset": "source:pmid:26981369", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Data is available in the Gene Expression Omnibus (GEO) [1], [2] accession GSE64375 through the direct link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE64375"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using Limma with a p-value cutoff of 0.05, the study identified approximately 400–500 differentially expressed genes at each radiation level relative to control; the raw CEL source files are available through GEO accession GSE64375.", "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:26981369"], "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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