Gene expression profiling can predict the fate of HeLa cells exposed to X-ray irradiation with or without protoporphyrin accumulation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484254", "kind": "science-record", "revision": 7, "content_hash": "sha256:7bef9f1407f5ed5f6ee8adfd1313f93a87b465e47275d305a59e6e1c3605aaa3", "created_at": "2026-11-01T15:40:13Z", "updated_at": "2026-11-01T21:58:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiling can predict the fate of HeLa cells exposed to X-ray irradiation with or without protoporphyrin accumulation.", "doi": "10.1016/j.gdata.2015.05.044", "pmid": "26484254", "authors": ["Junko Takahashi", "Masaki Misawa", "Hitoshi Iwahashi"], "journal": "Genomics data", "year": 2015, "abstract": "Protoporphyrin IX (PpIX) enhances the generation of reactive oxygen species in cells following physicochemical interactions with X-rays. To evaluate the use of porphyrins as radio-sensitizers in radiotherapy, the transcriptomic effects of PpIX and/or X-ray irradiation were investigated in HeLa cells. Microarray experiments were performed using Agilent-014,850 Whole Human Genome Microarray 4x44K G4112F (GEO#: GSE61805). We selected the condition corresponding to 1 μg/mL PpIX exposure prior to 3 Gy-irradiation of cells, and collected cells 24 h post irradiation. X-ray exposure at a dose of 3 Gy did not affect cell survival 24 h post irradiation, regardless of the concentration of PpIX. Approximately 50% cells exposed to X-ray irradiation alone (XT) and 70% cells exposed to PpIX treatment for 6 h before X-ray irradiation (PpIX-XT) lost clonogenic ability. Based on p-values (p < 0.01), we selected genes for functional analysis. The majority of the regulated genes in the XT and PpIX-XT groups were related to cell cycle arrest. Furthermore, transcriptome analysis of the cells collected 24 h post irradiation revealed the fate of the cells that lost clonogenic ability due to cell cycle arrest.", "claims": [{"id": "claim-method", "statement": "The Student's t-test was used to assess the significance of each gene in the microarray.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484254", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "The Student's t-test was used to assess the significance of each gene in the microarray."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Deposited data can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61805.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484254", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61805."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:26484254"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE61805"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE61805"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484254", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.05.044", "sha256": "sha256:0442ff10953a6e21810470e84c26aa65e5089c98dc974d9ab1ab91a6ad04407c", "bytes": 8472, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.05.044", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4583665", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE61805", "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=GSE61805", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE61805", "version": null, "note": "Deposited data can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61805.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Deposited data can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61805.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1514358", "GSM1514359", "GSM1514360", "GSM1514361", "GSM1514362", "GSM1514363", "GSM1514364", "GSM1514365", "GSM1514366", "GSM1514367", "GSM1514368", "GSM1514369"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Characterization of protoporphytin IX effects on X-ray irradiation in Hela cells in vitro", "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:26484254:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b7c1bb8be7da934e5f938bb13479cc5e608ee1a912639ab34427fc9a3b99e316", "bytes": 1050, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0015", "version": null, "note": null, "structure": {"pmcid": "PMC4583665", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Human/HeLa cell line"], ["Sex", "Female"], ["Sequence or array type", "Agilent-014,850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)"], ["Data format", "Raw data: TAR, Normalized data: TXT"], ["Experimental factors", "Gene expression profiling in HeLa cells with protoporphyrin IX treatment prior to X-ray irradiation (PpIX-XT), X-ray irradiation alone (XT), PpIX treatment alone (PpIXT), and non-treatment (NT)."], ["Experimental features", "The gene expression patterns of cells treated with 1 μg/mL and/or 3 Gy-irradiation collected 24 h after irradiation were analyzed. These specific conditions were chosen because X-ray exposure at a dose of 3 Gy did not affect cell survival 24 h post irradiation, but affected clonogenic survival regardless of the concentration of PpIX treatment."], ["Consent", "n/a"], ["Sample source location", "n/a"]], "row_count": 9, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0015"}}], "gaps": ["asset:data:geo:GSE61805 not downloaded", "asset:data:geo:GSE61805 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Student's t-test was used to assess the significance of each gene in the microarray."}}], "targets": [], "gaps": ["method.student_t"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE61805"], "resolved_accessions": ["GSE61805"], "statements": ["Deposited data can be found here: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61805."], "basis": "The paper names GSE61805 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:26484254", "data:geo:GSE61805", "asset:table:pmid:26484254:1"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE61805"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:06:35Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 7926, "completion_tokens": 1097, "cached_tokens": 768}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:26484254", "type": "paper", "label": "pmid:26484254"}, {"id": "source:pmid:26484254", "type": "manuscript", "label": "PMID 26484254 full text"}, {"id": "data:geo:GSE61805", "type": "dataset", "label": "GEO GSE61805"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484254", "type": "paper", "label": "pmid:26484254"}, {"id": "source:pmid:26484254", "type": "manuscript", "label": "PMID 26484254 full text"}, {"id": "data:geo:GSE61805", "type": "dataset", "label": "GEO GSE61805"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484254", "type": "extraction", "used": ["source:pmid:26484254"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE61805", "type": "accession_resolution", "used": ["data:geo:GSE61805"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:26484254", "parent_hash": "sha256:cdaade9532dd852176dca83e72a7b519ee911fd77d4bec60c9fe66e54b86ba9e", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE61805 licence not read", "asset:data:geo:GSE61805 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["expression profiling can predict the fate of HeLa cells exposed to X-ray irradiation with or w", "nd/or X-ray irradiation were investigated in HeLa cells. Microarray experiments were performed", "n Cell Bank (Tsukuba, Japan). The cells were cultured in DMEM containing 10% fetal bovine serum in a", "nd/or X-ray irradiation were investigated in HeLa cells. The present study employed microarray"], "order_basis": "paper_text_order:5", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["irradiation were investigated in HeLa cells. Microarray experiments were performed using Agilent-014", "med using Agilent-014,850 Whole Human Genome Microarray 4x44K G4112F (GEO#: GSE61805). We selected t", "ed in HeLa cells. The present study employed microarray analysis to quantify genes that were upregul", "0 μg/mL streptomycin. Sample preparation and microarray analyses RNA was extracted from cells using"], "order_basis": "paper_text_order:392", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Student's t-test was used to assess the significance of each gene in the microarray."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}