Specific transcriptional signature dataset of extracellular signal-regulated kinase 5 in leiomyosarcoma derived cell lines.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41233882", "kind": "science-record", "revision": 4, "content_hash": "sha256:1395c0810f08bb6520dfad1fdb6073ed6fc263827de80da4c44888e7f9f53b6e", "created_at": "2026-11-01T20:31:16Z", "updated_at": "2026-11-01T22:57:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Specific transcriptional signature dataset of extracellular signal-regulated kinase 5 in leiomyosarcoma derived cell lines.", "doi": "10.1186/s13104-025-07551-2", "pmid": "41233882", "authors": ["Jaime Jiménez-Suárez", "Cristina Garnés-García", "Pablo Fernández-Aroca", "Juan Aparicio-Canada", "Borja Belandia", "María José Ruiz-Hidalgo", "Ricardo Sánchez-Prieto", "Francisco J Cimas"], "journal": "BMC research notes", "year": 2025, "abstract": "OBJECTIVES: Soft-tissue sarcomas, particularly leiomyosarcomas, are aggressive tumors characterized by limited therapeutic options due to an insufficient understanding of their molecular drivers. To identify novel therapeutic targets, we investigated the role of Extracellular signal-regulated kinase-5 (ERK5), a critical signaling protein in soft-tissue sarcoma biology. The primary objective was to define the transcriptomic profile specifically associated with ERK5, enhancing the understanding of molecular mechanisms underlying leiomyosarcoma.\nDATA DESCRIPTION: Two uterine leiomyosarcoma cell lines, SK-UT-1 and AA, underwent ERK5 genetic knockdown via lentiviral transduction with shRNA followed by puromycin selection. Knockdown efficiency was confirmed through RT-qPCR and Western blotting. RNA sequencing was performed using the DNBSEQ platform. Raw reads underwent quality filtering and were aligned to the human genome (GRCh38.p13) with Bowtie2. Gene expression was quantified by RSEM, and differential expression analysis was conducted with DESeq2 (|log2FC|≥ 1, q-value ≤ 0.05). As a result, we identified 1218 and 227 differentially expressed genes for AA and SK-UT-1 respectively, and 81 in common for both cell lines. The raw and RNAseq data and sequences are available at the NCBI GEO repository under GSE297879. Sequence comparison could reveal new therapeutic targets based on the ERK5 signalling pathway, which is critical in experimental models of soft-tissue sarcoma.", "claims": [{"id": "claim-method", "statement": "Differential gene expression analysis was developed by DESeq2 (|log2FC| ≥ 1, q-value ≤ 0.05) [10].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41233882", "locator": "sections[2] \"Data description\" paragraph 3", "quote": "Differential gene expression analysis was developed by DESeq2 (|log2FC| ≥ 1, q-value ≤ 0.05) [10]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw RNA sequencing results for this publication are available from the NCBI Gene Expression Omnibus and are accessible through GEO Series accession number GSE297879 (https://identifiers.org/geo:GSE297879 [11]), . 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