Dataset for dose and time-dependent transcriptional response to ionizing radiation exposure.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31692674", "kind": "science-record", "revision": 8, "content_hash": "sha256:e7271b5168c6c16ffd6fce74cae5fd5dd6056f622444cf2c7c05c41718ed674f", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T22:44:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dataset for dose and time-dependent transcriptional response to ionizing radiation exposure.", "doi": "10.1016/j.dib.2019.104624", "pmid": "31692674", "authors": ["Eric C Rouchka", "Robert M Flight", "Bridgitte H Fasciotto", "Rosendo Estrada", "John W Eaton", "Phani K Patibandla", "Sabine J Waigel", "Dazhuo Li", "John K Kirtley", "Palaniappan Sethu", "Robert S Keynton"], "journal": "Data in brief", "year": 2019, "abstract": "Exposure to ionizing radiation associated with highly energetic and charged heavy particles is an inherent risk astronauts face in long duration space missions. We have previously considered the transcriptional effects that three levels of radiation (0.3 Gy, 1.5 Gy, and 3.0 Gy) have at an immediate time point (1 hr) post-exposure [1]. Our analysis of these results suggest effects on transcript levels that could be modulated at lower radiation doses [2]. In addition, a time dependent effect is likely to be present. Therefore, in order to develop a lab-on-a-chip approach for detection of radiation exposure in terms of both radiation level and time since exposure, we developed a time- and dose-course study to determine appropriate sensitive and specific transcript biomarkers that are detectable in blood samples. The data described herein was developed from a study measuring exposure to 0.15 Gy, 0.30 Gy, and 1.5 Gy of radiation at 1 hr, 2 hr, and 6 hr post-exposure using Affymetrix® GeneChip® PrimeView™ microarrays. This report includes raw gene expression data files from the resulting microarray experiments representing typical radiation exposure levels an astronaut may experience as part of a long duration space mission. The data described here is available in NCBI's Gene Expression Omnibus (GEO), accession GSE63952.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) (defined as Affymetrix® probesets) were determined using Limma [7].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31692674", "locator": "sections[6] \"Data acquisition\" paragraph 4", "quote": "Differentially expressed genes (DEGs) (defined as Affymetrix® probesets) were determined using Limma [7]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw and processed microarray data is available in the Gene Expression Omnibus (GEO) database at NCBI (GSE63952).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31692674", "locator": "sections[2] \"Data\" paragraph 2", "quote": "The raw and processed microarray data is available in the Gene Expression Omnibus (GEO) database at NCBI (GSE63952)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:31692674"], "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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the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6806397", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE63952", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63952", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63952", "version": null, "note": "The raw and processed microarray data is available in the Gene Expression Omnibus (GEO) database at NCBI (GSE63952).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw and processed microarray data is available in the Gene Expression Omnibus (GEO) database at NCBI (GSE63952).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1561166", "GSM1561167", "GSM1561168", "GSM1561169", "GSM1561170", "GSM1561171", "GSM1561172", "GSM1561173", "GSM1561174", "GSM1561175", "GSM1561176", "GSM1561177", "GSM1561178", "GSM1561179", "GSM1561180", "GSM1561181", "GSM1561182", "GSM1561183", "GSM1561184", "GSM1561185", "GSM1561186", "GSM1561187", "GSM1561188", "GSM1561189", "GSM1561190", "GSM1561191", "GSM1561192", "GSM1561193", "GSM1561194", "GSM1561195", "GSM1561196", "GSM1561197", "GSM1561198", "GSM1561199", "GSM1561200", "GSM1561201", "GSM1561202", "GSM1561203", "GSM1561204", "GSM1561205", "GSM1561206", "GSM1561207", "GSM1561208", "GSM1561209", "GSM1561210", "GSM1561211", "GSM1561212", "GSM1561213", "GSM1561214", "GSM1561215", "GSM1561216", "GSM1561217", "GSM1561218", "GSM1561219", "GSM1561220", "GSM1561221", "GSM1561222", "GSM1561223", "GSM1561224", "GSM1561225", "GSM1561226", "GSM1561227", "GSM1561228", "GSM1561229", "GSM1561230", "GSM1561231", "GSM1561232", "GSM1561233", "GSM1561234", "GSM1561235", "GSM1561236", "GSM1561237", "GSM1561238", "GSM1561239", "GSM1561240", "GSM1561241", "GSM1561242", "GSM1561243", "GSM1561244", "GSM1561245", "GSM1561246", "GSM1561247", "GSM1561248", "GSM1561249", "GSM1561250", "GSM1561251", "GSM1561252", "GSM1561253", "GSM1561254", "GSM1561255", "GSM1561256", "GSM1561257", "GSM1561258", "GSM1561259", "GSM1561260", "GSM1561261", "GSM1561262", "GSM1561263", "GSM1561264", "GSM1561265"], "sample_count": 100, "group_sizes": null, "group_sizes_basis": null, "platform": "15207", "taxon": "Homo sapiens", "title": "Early transcriptional changes in response to low dose radiation exposure", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31692674:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:53f0b7f5793859f98e04dd56b159e894fcb2400e9d7c4d528e555489833d711c", "bytes": 1786, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#undtbl1", "version": null, "note": "Specifications Table", "structure": {"pmcid": "PMC6806397", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": "Specifications Table", "rows": [["Subject", "Biochemistry, Genetics and Molecular Biology"], ["Specific subject area", "Cellular transcriptional response to radiation exposure"], ["Type of data", "Microarray gene expression data"], ["How data were acquired", "Affymetrix® GeneChip® PrimeView™ Arrays"], ["Data format", "Raw; CEL files"], ["Experimental Factors", "0.15 Gy vs. 0.0 Gy at 1 hr post-exposure0.15 Gy vs. 0.0 Gy at 2 hr post-exposure0.15 Gy vs. 0.0 Gy at 6 hr post-exposure0.30 Gy vs. 0.0 Gy at 1 hr post-exposure0.30 Gy vs. 0.0 Gy at 2 hr post-exposure0.30 Gy vs. 0.0 Gy at 6 hr post-exposure1.50 Gy vs. 0.0 Gy at 1 hr post-exposure1.50 Gy vs. 0.0 Gy at 2 hr post-exposure1.50 Gy vs. 0.0 Gy at 6 hr post-exposure0.15 Gy vs. 0.0 Gy (dose-dependent)0.30 Gy vs. 0.0 Gy (dose-dependent)1.50 Gy vs. 0.0 Gy (dose-dependent)2 hr vs. 1 hr (time-dependent)6 hr vs. 1 hr (time-dependent)"], ["Experimental Features", "Gene expression profiling of radiation exposure using:1.0 Gy, 1 hr post-exposure (control; n = 10);1.0 Gy, 2 hr post-exposure (n = 10);1.0 Gy, 6 hr post-exposure (n = 5);0.15 Gy, 1 hr post-exposure (n = 10);0.15 Gy, 2 hr post-exposure (n = 10);0.15 Gy, 6 hr post-exposure (n = 5);0.30 Gy, 1 hr post-exposure (n = 10);0.30 Gy, 2 hr post-exposure (n = 10);0.30 Gy, 6 hr post-exposure (n = 5);1.50 Gy, 1 hr post-exposure (n = 10);1.50 Gy, 2 hr post-exposure (n = 10);1.50 Gy, 6 hr post-exposure (n = 5)."], ["Data source location", "Louisville, Kentucky USA"], ["Data accessibility", "Repository name: Gene Expression Omnibus (GEO)Data identification number: GSE63952Direct URL to data: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63952"]], "row_count": 9, "column_count": 2, "numeric_cells": 3, "header_rows": 0, "locator": "section[1]/table-wrap[1]#undtbl1"}}, {"id": "asset:table:pmid:31692674:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cac2ea85db4c3a3e80765ccef8b0b0a6fdb4e75c47fc87954b13f349e8f2f3f4", "bytes": 1309, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[2]#undtbl2", "version": null, "note": null, "structure": {"pmcid": "PMC6806397", "section_index": 1, "section_title": "p", "row_count": 1, "column_count": 1}, "table": {"label": null, "caption": null, "rows": [["Value of the Data•Few high-throughput studies regarding ionizing radiation exposure are publicly available. This dataset provides novel time- and dose-dependent transcript abundance data based on typical ionizing radiation exposure faced by astronauts at 0.15 Gy, 0.30 Gy, and 1.50 Gy.•Evaluation of time since exposure is possible with this dataset at immediate time points (1 hr and 2hr post-exposure) as well as an intermediate time point (6 hr post-exposure). Used together, these results allow for the design of appropriate transcript biomarkers used to determine radiation exposure events, the amount of radiation exposed, and the time since the event. As a result, this data can allow for design of appropriate treatment and mitigation.•The determination of appropriate biomarkers for general radiation exposure, dose-dependent markers, and time-dependent markers within blood plasma samples makes it possible to design light-weight, portable, lab-on-a-chip diagnostic tests for measuring radiation exposure. Such diagnostic instrumentation can be incorporated on long-term space flights in order to properly address radiation exposure events."]], "row_count": 1, "column_count": 1, "numeric_cells": 1, "header_rows": 0, "locator": "section[1]/table-wrap[2]#undtbl2"}}, {"id": "asset:table:pmid:31692674:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a6cd42ae340d1bd244a756833217ba67133d8af9c07f3a6877f4e7c32cc97f1f", "bytes": 5248, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[1]#tbl1", "version": null, "note": "Sample information.", "structure": {"pmcid": "PMC6806397", "section_index": 2, "section_title": "Data", "row_count": 51, "column_count": 8}, "table": {"label": "Table 1", "caption": "Sample information.", "rows": [["Volunteer", "Time", "Dose", "SampleName", "GEOSample ID", "Dose", "SampleName", "GEOSample ID"], ["1", "1 hr", "0 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as the number of differentially expressed probes detected by Limma at p ≤ 0.05 for low (0.15 Gy vs. 0.0 Gy), mid (0.30 Gy vs. 0.0 Gy) and high (1.5 vs. 0.0 Gy) radiation levels at early (1 hr), mid (2 hr), and late (6 hr) as well as combined time points. Arrows indicate the number of up (↑) or down (↓) regulated probesets.", "structure": {"pmcid": "PMC6806397", "section_index": 2, "section_title": "Data", "row_count": 6, "column_count": 4}, "table": {"label": "Table 2", "caption": "Radiation dependent differentially expressed genes measured as the number of differentially expressed probes detected by Limma at p ≤ 0.05 for low (0.15 Gy vs. 0.0 Gy), mid (0.30 Gy vs. 0.0 Gy) and high (1.5 vs. 0.0 Gy) radiation levels at early (1 hr), mid (2 hr), and late (6 hr) as well as combined time points. Arrows indicate the number of up (↑) or down (↓) regulated probesets.", "rows": [["Time Point", "Comparison"], ["0.15 Gy vs 0 Gy", "0.30 Gy vs 0 Gy", "1.5 Gy vs 0 Gy"], ["Early (1hr)", "879 (635↑, 244↓)", "1462 (898↑, 564↓)", "2278 (1423↑, 855↓)"], ["Mid (2 hr)", "905 (446↑,459↓)", "1521 (763↑,758↓)", "3575 (2115↑,1460↓)"], ["Late (6 hr)", "841 (510↑,331↓)", "1461 (776↑,685↓)", "1884 (1177↑,707↓)"], ["Combined", "805 (496↑,309↓)", "1913 (970↑,943↓)", "3289 (1815↑,1474↓)"]], "row_count": 6, "column_count": 4, "numeric_cells": 18, "header_rows": 2, "locator": "section[2]/table-wrap[2]#tbl2"}}, {"id": "asset:table:pmid:31692674:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:264b968f86efb1428b83437094b0953d89556253ee1eb5087cfd1b7c584226a3", "bytes": 978, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[3]#tbl3", "version": null, "note": "Time dependent differentially expressed genes measured as the number of differentially expressed probesets detected by Limma at p ≤ 0.05 and a log fold-change cutoff of 1 for mid (2 hr vs. 1 hr) and late (6 hr vs. 1 hr) time points measured with no radiation (0 Gy), low radiation (0.15 Gy), mid radiation (0.30 Gy) and high radiation (1.5 Gy) as well as all radiation levels combined. Arrows indicate the number of up (↑) or down (↓) regulated probesets.", "structure": {"pmcid": "PMC6806397", "section_index": 2, "section_title": "Data", "row_count": 7, "column_count": 3}, "table": {"label": "Table 3", "caption": "Time dependent differentially expressed genes measured as the number of differentially expressed probesets detected by Limma at p ≤ 0.05 and a log fold-change cutoff of 1 for mid (2 hr vs. 1 hr) and late (6 hr vs. 1 hr) time points measured with no radiation (0 Gy), low radiation (0.15 Gy), mid radiation (0.30 Gy) and high radiation (1.5 Gy) as well as all radiation levels combined. 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