Transcriptome Analysis of Myocardial Ischemic-Hypoxic Injury in Rats and Hypoxic H9C2 Cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39010664", "kind": "science-record", "revision": 2, "content_hash": "sha256:c51d833cae64f15b0984ba943e93e91dbd2d1e96e225ce0f1e298ac449ea5a19", "created_at": "2026-11-01T20:29:05Z", "updated_at": "2026-11-01T21:33:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptome Analysis of Myocardial Ischemic-Hypoxic Injury in Rats and Hypoxic H9C2 Cells.", "doi": "10.1002/ehf2.14903", "pmid": "39010664", "authors": ["Nan Niu", "Huangtai Miao", "Hongmei Ren"], "journal": "ESC heart failure", "year": 2024, "abstract": "AIMS: This study aimed to address inconsistencies in results between the H9C2 myocardial hypoxia (MH) cell line and myocardial infarction (MI) rat models used in MI research. We identified differentially expressed genes (DEGs) and underlying molecular mechanisms using RNA sequencing technology.\nMETHODS: RNA sequencing was used to analyse DEGs in MI rat tissues and H9C2 cells exposed to hypoxia for 24 h. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to identify key biological processes and pathways. Weighted correlation network analysis [weighted gene co-expression network analysis (WGCNA)] was used to construct gene co-expression networks, and hub genes were compared with published MI datasets [Gene Expression Omnibus (GEO)] for target identification.\nRESULTS: GO analysis revealed enrichment of immune inflammation and mitochondrial respiration processes among 5139 DEGs in MI tissues and 2531 in H9C2 cells. KEGG analysis identified 537 overlapping genes associated with metabolism and oxidative stress pathways. Cross-analyses using the published GSE35088 and GSE47495 datasets identified 40 and 16 overlapping genes, respectively, with nine genes overlapping across all datasets and our models. WGCNA identified a key module in the MI model enriched for mRNA processing and protein binding. GO analysis revealed enrichment of mRNA processing, protein binding and mitochondrial respiratory chain complex I assembly in MI and H9C2 MH models. Five relevant hub genes were identified via a cross-analysis between the 92 hub genes that showed a common expression trend in both models.\nCONCLUSIONS: This study reveals both shared and distinct transcriptomic responses in the MI and H9C2 models, highlighting the importance of model selection for studying myocardial ischaemia and hypoxia.", "claims": [{"id": "claim-method", "statement": "Weighted correlation network analysis [weighted gene co‐expression network analysis (WGCNA)] was used to construct gene co‐expression networks, and hub genes were compared with published MI datasets [Gene Expression Omnibus (GEO)] for target identification.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39010664", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Weighted correlation network analysis [weighted gene co‐expression network analysis (WGCNA)] was used to construct gene co‐expression networks, and hub genes were compared with published MI datasets [Gene Expression Omnibus (GEO)] for target identification."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analysed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39010664", "locator": "sections[31] \"Data availability statement\" paragraph 2", "quote": "All data generated or analysed during this study are included in this published article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Five relevant hub genes were identified by cross-analysis of 92 hub genes that showed a common expression trend in the MI and H9C2 myocardial hypoxia models.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39010664", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Five relevant hub genes were identified via a cross‐analysis between the 92 hub genes that showed a common expression trend in both models."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Five relevant hub genes were identified by cross-analysis of 92 hub genes that showed a common expression trend in the MI and H9C2 myocardial hypoxia models.", "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:39010664"], "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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