Gene expression profiling of DBA/2J mice cochleae treated with l-methionine and valproic acid.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484279", "kind": "science-record", "revision": 6, "content_hash": "sha256:cdc9300e3e0aab930d405a13f5587fdccca500e8923beec833d17e17c6affd3d", "created_at": "2026-11-01T15:40:13Z", "updated_at": "2026-11-01T21:20:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiling of DBA/2J mice cochleae treated with l-methionine and valproic acid.", "doi": "10.1016/j.gdata.2015.06.022", "pmid": "26484279", "authors": ["Fuyuki Miya", "Hideki Mutai", "Masato Fujii", "Keith A Boroevich", "Tatsuo Matsunaga", "Tatsuhiko Tsunoda"], "journal": "Genomics data", "year": 2015, "abstract": "DBA/2J mice, which have homozygous mutations in Cdh23 and Fscn2, are characterized by early onset hearing loss at as early as three-weeks of age (Noben-Trauth et al., 2003 [1]) and are an animal model for progressive hearing loss research. Recently, it has been reported that epigenetic regulatory pathways likely play an important role in hearing loss (Provenzano and Domann, 2007 [2]; Mutai et al., 2009 [3]; Waldhaus et al., 2012 [4]). We previously reported that DBA/2J mice injected subcutaneously with a combination of epigenetic modifying reagents, l-methionine (MET) as methyl donor and valproic acid (VPA) as a pan-histone deacetylases (Hdac) inhibitor, showed a significant attenuation of progressive hearing loss by measuring their auditory brainstem response (ABR) thresholds (Mutai et al., 2015 [5]). Here we present genome wide expression profiling of the DBA/2J mice cochleae, with and without treatment of MET and VPA, to identify the genes involved in the reduction of progressive hearing loss. The raw and normalized data were deposited in NCBI's Gene Expression Omnibus (GEO ID: GSE62173) for ease of reproducibility and reanalysis.", "claims": [{"id": "claim-method", "statement": "To identify possible genes involved in attenuation of progressive hearing loss induced by MET and VPA, we compared the cochleae expression of MET + VPA to the vehicle control group using Welch's two-side t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484279", "locator": "sections[8] \"Differentially expressed genes and cluster analysis\" paragraph 2", "quote": "To identify possible genes involved in attenuation of progressive hearing loss induced by MET and VPA, we compared the cochleae expression of MET + VPA to the vehicle control group using Welch's two-side t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw and normalized data were deposited in NCBI's Gene Expression Omnibus (GEO ID: GSE62173) for ease of reproducibility and reanalysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484279", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw and normalized data were deposited in NCBI's Gene Expression Omnibus (GEO ID: GSE62173) for ease of reproducibility and reanalysis."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper identified 49 up-regulated and 195 down-regulated genes in MET + VPA-treated DBA/2J cochleae using Welch's two-side t-test, and deposited the raw and normalized microarray data in GEO under accession GSE62173.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484279", "locator": "sections[8] \"Differentially expressed genes and cluster analysis\" paragraph 2", "quote": "To identify possible genes involved in attenuation of progressive hearing loss induced by MET and VPA, we compared the cochleae expression of MET + VPA to the vehicle control group using Welch's two-side t-test."}, {"asset": "source:pmid:26484279", "locator": "sections[8] \"Differentially expressed genes and cluster analysis\" paragraph 2", "quote": "Using these criteria, 55 probes (49 genes) and 244 probes (195 genes) were up- and down-regulated in the MET + VPA group, respectively (Fig. 2)."}, {"asset": "source:pmid:26484279", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The raw and normalized data were deposited in NCBI's Gene Expression Omnibus (GEO ID: GSE62173) for ease of reproducibility and reanalysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper identified 49 up-regulated and 195 down-regulated genes in MET + VPA-treated DBA/2J cochleae using Welch's two-side t-test, and deposited the raw and normalized microarray data in GEO under accession GSE62173.", "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:26484279"], "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:GSE62173"], "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:GSE62173"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26484279", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.gdata.2015.06.022", "sha256": "sha256:e95029511a24b8764848c43afd7521e0b5ce273b8a7fa05797a4c8899275d451", "bytes": 8262, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.gdata.2015.06.022", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4583681", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE62173", "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=GSE62173", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62173", "version": null, "note": "The raw and normalized data were deposited in NCBI's Gene Expression Omnibus (GEO ID: GSE62173) for ease of reproducibility and reanalysis.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The raw and normalized data were deposited in NCBI's Gene Expression Omnibus (GEO ID: GSE62173) for ease of reproducibility and reanalysis.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1520965", "GSM1520966", "GSM1520967", "GSM1520968", "GSM1520969", "GSM1520970", "GSM1520971", "GSM1520972", "GSM1520973", "GSM1520974", "GSM1520975", "GSM1520976", "GSM1520977", "GSM1520978", "GSM1520979", "GSM1520980"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "1261", "taxon": "Mus musculus", "title": "Expression data of mice cochlea treated with L-methionine and valproic acid.", "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:26484279:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f55853e2947233c8af0fc84d86cdc0ba7a8db23998023ea19df144bcd061e4f4", "bytes": 945, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0005", "version": null, "note": null, "structure": {"pmcid": "PMC4583681", "section_index": 1, "section_title": "p", "row_count": 9, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Specifications"], ["Organism/cell line/tissue", "Mus musculus (DBA/2J)"], ["Sex", "Male"], ["Sequencer or array type", "Affymetrix GeneChip Mouse Genome 430 2.0 Array"], ["Data format", "Raw data: CEL files, normalized data: SOFT, MINiML and TXT files"], ["Experimental factors", "DBA/2J mice at 4 weeks of age (untreated), 12 week old mice treated with control vehicle (0.1 M sodium bicarbonate) for 8 weeks, and 12 week old mice treated with l-methionine and valproic acid were analyzed."], ["Experimental features", "Microarray gene expression profiling to identify transcripts that are regulated by l-methionine and valproic acid in cochleae of DBA/2J mice as an animal model for hearing loss"], ["Consent", "Not applicable"], ["Sample source location", "Mice were purchased from Clea Japan (Tokyo, Japan)."]], "row_count": 9, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[1]/table-wrap[1]#t0005"}}], "gaps": ["asset:data:geo:GSE62173 not downloaded", "asset:data:geo:GSE62173 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "welch_t_test", "label": "Group comparison", "dsl_operations": ["welch_t"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To identify possible genes involved in attenuation of progressive hearing loss induced by MET and VPA, we compared the cochleae expression of MET + VPA to the vehicle control group using Welch's two-side t-test."}}], "targets": [], "gaps": []}, "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": true, "required_operations": ["welch_t"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: welch_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": ["GSE62173"], "resolved_accessions": ["GSE62173"], "statements": ["The raw and normalized data were deposited in NCBI's Gene Expression Omnibus (GEO ID: GSE62173) for ease of reproducibility and reanalysis."], "basis": "The paper names GSE62173 in NCBI's Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["welch_t"], "assets": ["source:pmid:26484279", "data:geo:GSE62173", "asset:table:pmid:26484279:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE62173"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:59Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 20943, "completion_tokens": 2757, "cached_tokens": 2096}}, "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:26484279", "type": "paper", "label": "pmid:26484279"}, {"id": "source:pmid:26484279", "type": "manuscript", "label": "PMID 26484279 full text"}, {"id": "data:geo:GSE62173", "type": "dataset", "label": "GEO GSE62173"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26484279", "type": "paper", "label": "pmid:26484279"}, {"id": "source:pmid:26484279", "type": "manuscript", "label": "PMID 26484279 full text"}, {"id": "data:geo:GSE62173", "type": "dataset", "label": "GEO GSE62173"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26484279", "type": "extraction", "used": ["source:pmid:26484279"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE62173", "type": "accession_resolution", "used": ["data:geo:GSE62173"], "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:26484279", "parent_hash": "sha256:afc72496e459c242fea93671f2875ec751067f9fafabc5d2a3778ee65d5817f0", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE62173 licence not read", "asset:data:geo:GSE62173 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e hearing loss. Animals and treatment DBA/2J mice were purchased from Clea Japan (Tokyo, Japan). Mi", "re purchased from Clea Japan (Tokyo, Japan). Mice were housed in plastic cages with metallic lid in", "(MET + VPA, Fig. 1). The age-matched control mice were male DBA/2J mice of 4-weeks old subcutaneous", "sive hearing loss was observed and validated in mice injected with MET and VPA as previously repo"], "order_basis": "paper_text_order:2169", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["welch_t"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["To identify possible genes involved in attenuation of progressive hearing loss induced by MET and VPA, we compared the cochleae expression of MET + VPA to the vehicle control group using Welch's two-side t-test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}