Expression-profiling of apoptosis induced by ablation of the long ncRNA TRPM2-AS in prostate cancer cell.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484139", "kind": "science-record", "revision": 2, "content_hash": "sha256:60e69150f13eab89bad4d5a3af30117470e609ae06558ba40842a4cfdbca0333", "created_at": "2026-11-01T15:40:11Z", "updated_at": "2026-11-01T18:47:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Expression-profiling of apoptosis induced by ablation of the long ncRNA TRPM2-AS in prostate cancer cell.", "doi": "10.1016/j.gdata.2014.10.020", "pmid": "26484139", "authors": ["Giovanni Lavorgna", "Fulvio Chiacchiera", "Alberto Briganti", "Francesco Montorsi", "Diego Pasini", "Andrea Salonia"], "journal": "Genomics data", "year": 2015, "abstract": "We recently identified the long non-coding RNA (ncRNA) TRPM2-AS as a key regulator of survival in prostate cancer [1]. This essential role, coupled to the TRPM2-AS low-expression levels in healthy tissues, makes this ncRNA a suitable therapeutic target for further clinical studies. To get insights into the survival mechanism controlled by this molecule, we ablated its expression in prostate cancer cells and performed a genome-wide analysis of the transcripts differentially regulated in dying cells. Here, we describe in detail the experimental system, methods and quality control for the generation of the microarray data associated with our recent publication [1]. The data are related to [1]. Data have been deposited to the Gene Expression Omnibus (GEO) database repository with the dataset identifier GSE40687.", "claims": [{"id": "claim-data-access", "statement": "Microarray data is deposited at the NCBI Gene Expression Omnibus (GEO) database under GEO Series and is available at the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40687.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484139", "locator": "sections[2] \"Direct link to the deposited data\" paragraph 2", "quote": "Microarray data is deposited at the NCBI Gene Expression Omnibus (GEO) database under GEO Series and is available at the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40687."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The microarray results were validated by qRT-PCR with a correlation coefficient of 0.97, and the source data are deposited in GEO under accession GSE40687.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484139", "locator": "sections[6] \"Microarray and quality control\" paragraph 2", "quote": "Results, shown in Fig. 1, indicated that while, due to the large dynamic range of qRT-PCR [6], microarray data were mostly slightly compressed, there was an excellent qualitative correlation among the two techniques (correlation coefficient: 0.97), thereby validating the microarray experiment."}, {"asset": "source:pmid:26484139", "locator": "sections[2] \"Direct link to the deposited data\" paragraph 2", "quote": "Microarray data is deposited at the NCBI Gene Expression Omnibus (GEO) database under GEO Series and is available at the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40687."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The microarray results were validated by qRT-PCR with a correlation coefficient of 0.97, and the source data are deposited in GEO under accession GSE40687.", "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:26484139"], "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:GSE40687"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:GSE40687"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484139", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2014.10.020", "sha256": "sha256:735fcc6d7d287e9ef8c6e1651497820bd573db87c0ddcbdfabb676ca5cb018b0", "bytes": 6293, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2014.10.020", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4535459", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE40687", "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=GSE40687", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40687", "version": null, "note": "Microarray data is deposited at the NCBI Gene Expression Omnibus (GEO) database under GEO Series and is available at the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40687.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Microarray data is deposited at the NCBI Gene Expression Omnibus (GEO) database under GEO Series and is available at the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40687.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM999201", "GSM999202", "GSM999203", "GSM999204", "GSM999205", "GSM999206", "GSM999207", "GSM999208"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "The effect of TRPM2-AS depletion in human prostate carcinoma PC3 cell line", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE40687 not downloaded", "asset:data:geo:GSE40687 licence not read"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "operations"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (not named), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE40687"], "resolved_accessions": ["GSE40687"], "statements": ["Microarray data is deposited at the NCBI Gene Expression Omnibus (GEO) database under GEO Series and is available at the following link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40687."], "basis": "The paper names GSE40687 in NCBI 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:26484139", "data:geo:GSE40687"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE40687"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:16Z", "independence": "same_provider"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 17194, "completion_tokens": 2147, "cached_tokens": 1552}}, "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:26484139", "type": "paper", "label": "pmid:26484139"}, {"id": "source:pmid:26484139", "type": "manuscript", "label": "PMID 26484139 full text"}, {"id": "data:geo:GSE40687", "type": "dataset", "label": "GEO GSE40687"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484139", "type": "paper", "label": "pmid:26484139"}, {"id": "source:pmid:26484139", "type": "manuscript", "label": "PMID 26484139 full text"}, {"id": "data:geo:GSE40687", "type": "dataset", "label": "GEO GSE40687"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484139", "type": "extraction", "used": ["source:pmid:26484139"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE40687", "type": "accession_resolution", "used": ["data:geo:GSE40687"], "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:26484139", "parent_hash": "sha256:0a82ccce70e050a33f52bb8d5599c04c57c2d491323292d1190145adbf3b78ee", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE40687 licence not read", "asset:data:geo:GSE40687 not downloaded", "execution.not_run", "method", "operations", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["Expression-profiling of apoptosis induced by ablation of the long ncRNA TRPM2-"], "order_basis": "paper_text_order:0", "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": 0.93, "evidence": ["nd quality control for the generation of the microarray data associated with our recent publication"], "order_basis": "paper_text_order:672", "id": "assay:2"}]}