Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30611906", "kind": "science-record", "revision": 8, "content_hash": "sha256:e14a8ed144bf09a3627f298ea0dc56ce8c99639d95d4d8bd03a7f2334141ec45", "created_at": "2026-11-01T15:40:40Z", "updated_at": "2026-11-01T22:43:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage.", "doi": "10.1016/j.joca.2018.12.015", "pmid": "30611906", "authors": ["B Ajekigbe", "K Cheung", "Y Xu", "A J Skelton", "A Panagiotopoulos", "J Soul", "T E Hardingham", "D J Deehan", "M J Barter", "D A Young"], "journal": "Osteoarthritis and cartilage", "year": 2019, "abstract": "OBJECTIVE: Long intergenic non-coding RNAs (lincRNAs) are emerging as key regulators in gene expression; however, little is known about the lincRNA expression changes that occur in osteoarthritis (OA). Here we aimed to define a transcriptome of lncRNAs in OA cartilage, specifically comparing the lincRNA transcriptome of knee and hip cartilage.\nMETHOD: RNA-seq was performed on nucleic acid extracted from hip cartilage from patients undergoing joint replacement surgery because of either OA (n = 10) or because of a neck of femur fracture (NOF; n = 6). After transcript alignment, counts were performed using Salmon and differential expression for ENSEMBL lincRNAs determined using DESeq2. Hip RNA-seq lincRNA expression was compared to a knee dataset (ArrayExpress; E-MTAB-4304). ChIP-seq data from ENCODE was used to determine whether lincRNAs were associated with promoters (plncRNA) or unidirectional enhancer-like regulatory elements (elncRNAs).\nRESULTS: Our analysis of the hip transcriptome identified 1692 expressed Transcripts Per Million (TPM ≥1) Ensembl lincRNAs, of which 198 were significantly (FDR ≤0.05) differentially expressed in OA vs normal (NOF) cartilage. Similar analysis of knee cartilage transcriptome identified 648 Emsembl lincRNAs with 93 significantly (FDR ≤0.05) differentially expressed in intact vs damaged cartilage. In total, 1834 lincRNAs were expressed in both hip and knee cartilage, with a highly significant correlation in expression between the two cartilages.\nCONCLUSION: This is the first study to use RNA-seq to map and compare the lincRNA transcriptomes of hip and knee cartilage. We propose that lincRNAs expressed selectively in cartilage, or showing differential expression in OA, will play a role in cartilage homoeostasis.", "claims": [{"id": "claim-method", "statement": "After transcript alignment, counts were performed using Salmon and differential expression for ENSEMBL lincRNAs determined using DESeq2. Hip RNA-seq lincRNA expression was compared to a knee dataset (ArrayExpress; E-MTAB-4304).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30611906", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "After transcript alignment, counts were performed using Salmon and differential expression for ENSEMBL lincRNAs determined using DESeq2. Hip RNA-seq lincRNA expression was compared to a knee dataset (ArrayExpress; E-MTAB-4304)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Fastq files are available to download from the National Center for Biotechnology Information Expression Omnibus GSE111358.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30611906", "locator": "sections[4] \"RNA extraction and sequencing\" paragraph 2", "quote": "Fastq files are available to download from the National Center for Biotechnology Information Expression Omnibus GSE111358."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30611906"], "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:E-MTAB-4304"], "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:E-MTAB-4304"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30611906", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.joca.2018.12.015", "sha256": 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["ENSG00000214548", "MEG3", "381.13", "30.04", "−0.864", "1.350", "1.25E-03", "4.23E-11"], ["ENSG00000261200", "RP11-989E6.10", "5.91", "0.55", "−0.629", "0.719", "1.43E-03", "1.25E-02"], ["ENSG00000235815", "RP1-125N5.2", "8.95", "9.94", "1.220", "0.684", "1.56E-03", "3.14E-03"], ["ENSG00000230606", "AC159540.1", "32.76", "14.93", "0.504", "0.646", "1.72E-03", "5.21E-03"], ["ENSG00000179523", "EIF3J-AS1", "21.25", "17.74", "−0.405", "0.322", "2.01E-03", "6.31E-03"], ["ENSG00000212694", "LINC01089", "20.08", "14.49", "0.421", "0.792", "2.21E-03", "3.01E-06"], ["ENSG00000272374", "RP3-329A5.8", "0.61", "0.23", "−0.746", "0.849", "3.07E-03", "1.29E-02"], ["ENSG00000203709", "C1orf132", "8.65", "0.65", "−1.058", "0.462", "3.28E-03", "1.88E-02"], ["ENSG00000224652", "LINC00885", "0.99", "0.94", "0.887", "0.713", "5.05E-03", "8.52E-03"], ["ENSG00000230487", "PSMG3-AS1", "4.77", "2.51", "0.625", "0.504", "7.08E-03", "7.18E-03"], ["ENSG00000245532", "NEAT1", "1149.80", "250.31", "−0.865", 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METHOD: RNA-seq was performed on nucleic acid extracted from", "NSEMBL lincRNAs determined using DESeq2. Hip RNA-seq lincRNA expression was compared to a knee da", ". CONCLUSION: This is the first study to use RNA-seq to map and compare the lincRNA transcriptome", "Scatter plot of lincRNA counts in OA vs NOF RNA-seq. Significant lincRNAs (DESeq2, FDR < 0.05) a"], "order_basis": "paper_text_order:400", "id": "assay:1"}, {"role": "data_generation", "definition_id": "chip_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["a knee dataset (ArrayExpress; E-MTAB-4304). 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