Transcriptomic profiling of cartilage ageing.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26484061", "kind": "science-record", "revision": 8, "content_hash": "sha256:a751b6c439f4a3b9d6957d9041344ccc59f0c3dc11ff24a3ab8fadc4acd05158", "created_at": "2026-11-01T15:40:11Z", "updated_at": "2026-11-01T22:42:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic profiling of cartilage ageing.", "doi": "10.1016/j.gdata.2014.03.001", "pmid": "26484061", "authors": ["Mandy Jayne Peffers", "Xuan Liu", "Peter David Clegg"], "journal": "Genomics data", "year": 2014, "abstract": "The musculoskeletal system is severely affected by the ageing process, with many tissues undergoing changes that lead to loss of function and frailty. Articular cartilage is susceptible to age related diseases, such as osteoarthritis. Applying RNA-Seq to young and old equine cartilage, we identified an over-representation of genes with reduced expression relating to extracellular matrix, degradative proteases, matrix synthetic enzymes, cytokines and growth factors in cartilage from older donors. Here we describe the contents and quality controls in detail for the gene expression and related results published by Peffers and colleagues in Arthritis Research and Therapy 2013 associated with the data uploaded to ArrayExpress (E-MTAB-1386).", "claims": [{"id": "claim-method", "statement": "Differential gene expression analysis was applied to the read count data for reads mapped to annotated genes using the R (version 2.15.1) Bioconductor package edgeR (version 2.13.0) [5].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484061", "locator": "sections[6] \"Data processing and normalisation\" paragraph 2", "quote": "Differential gene expression analysis was applied to the read count data for reads mapped to annotated genes using the R (version 2.15.1) Bioconductor package edgeR (version 2.13.0) [5]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All sequence data produced in this study has been submitted to NCBI GEO under Array Express accession number E-MTAB-1386.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484061", "locator": "sections[6] \"Data processing and normalisation\" paragraph 2", "quote": "All sequence data produced in this study has been submitted to NCBI GEO under Array Express accession number E-MTAB-1386."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The expression of 396 transcribed elements including mRNAs, small non-coding RNAs, pseudogenes, and a single microRNA was significantly different in old compared to young cartilage.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Genes were deemed differentially expressed with a Benjamini–Hochberg false discovery rate (FDR)-corrected p-value < 0.05 and fold change ≥ 1.4log2 [7] using a generalised linear model (GLM) likelihood ratio test."}, "evidence": [{"asset": "source:pmid:26484061", "locator": "sections[6] \"Data processing and normalisation\" paragraph 2", "quote": "Differential gene expression analysis was applied to the read count data for reads mapped to annotated genes using the R (version 2.15.1) Bioconductor package edgeR (version 2.13.0) [5]."}, {"asset": "source:pmid:26484061", "locator": "sections[6] \"Data processing and normalisation\" paragraph 2", "quote": "Genes were deemed differentially expressed with a Benjamini–Hochberg false discovery rate (FDR)-corrected p-value < 0.05 and fold change ≥ 1.4log2 [7] using a generalised linear model (GLM) likelihood ratio test."}, {"asset": "source:pmid:26484061", "locator": "sections[6] \"Data processing and normalisation\" paragraph 2", "quote": "All sequence data produced in this study has been submitted to NCBI GEO under Array Express accession number E-MTAB-1386."}, {"asset": "source:pmid:26484061", "locator": "sections[2] \"Direct link to deposited data\" paragraph 2", "quote": "Deposited data can be found at: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1386/."}, {"asset": "source:pmid:26484061", "locator": "sections[6] \"Data processing and normalisation\" paragraph 5", "quote": "The expression of 396 transcribed elements including mRNAs, small non-coding RNAs, pseudogenes, and a single microRNA was significantly different in old compared to young cartilage. Of these, 93 were at higher levels in the older cartilage and 303 were at lower levels in the older cartilage."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The expression of 396 transcribed elements including mRNAs, small non-coding RNAs, pseudogenes, and a single microRNA was significantly different in old compared to young cartilage.", "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:26484061"], "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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