Noncoding RNAs in human intervertebral disc degeneration: An integrated microarray study.

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The striking findings of miRNAs (microRNAs) and lncRNAs (long noncoding RNAs) as members of noncoding RNAs open up an exciting era in the studies of gene regulation. More recently, the reports of circRNAs (circular RNAs) add fuel to the noncoding RNAs research. Human intervertebral disc degeneration (IDD) is a main cause of low back pain as a disabling spinal disease. We have addressed the expression profiles if miRNAs, lncRNAs and mRNAs in IDD (Wang et al., J Pathology, 2011 and Wan et al., Arthritis Res Ther, 2014). Furthermore, we thoroughly analysed noncoding RNAs, including miRNAs, lncRNAs and circRNAs in IDD using the very same samples. Here we delineate in detail the contents of the aforementioned microarray analyses. Microarray and sample annotation data were deposited in GEO under accession number GSE67567 as SuperSeries. The integrated analyses of these noncoding RNAs will shed a novel light on coding-noncoding regulatory machinery.", "claims": [{"id": "claim-method", "statement": "Differentially expressed noncoding RNAs and mRNAs between two groups were identified through fold-change filtering and Student's t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484230", "locator": "sections[7] \"Normalization and data analysis\" paragraph 3", "quote": "Differentially expressed noncoding RNAs and mRNAs between two groups were identified through fold-change filtering and Student's t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Microarray and sample annotation data were deposited in GEO under accession number GSE67567 as SuperSeries.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26484230", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Microarray and sample annotation data were deposited in GEO under accession number GSE67567 as SuperSeries."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used quantile normalization and Benjamini-Hochberg false discovery rate correction for statistical analysis of noncoding RNA and mRNA microarray data, with raw and annotated data accessible through GEO SuperSeries accession GSE67567.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26484230", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The integrated analyses of these noncoding RNAs will shed a novel light on coding-noncoding regulatory machinery."}, {"asset": "source:pmid:26484230", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Microarray and sample annotation data were deposited in GEO under accession number GSE67567 as SuperSeries."}, {"asset": "source:pmid:26484230", "locator": "sections[7] \"Normalization and data analysis\" paragraph 2", "quote": "Quantile normalization and subsequent data processing were performed with the Gene Spring GX v11.5.1 software package (Agilent Technologies)."}, {"asset": "source:pmid:26484230", "locator": "sections[7] \"Normalization and data analysis\" paragraph 3", "quote": "Differentially expressed noncoding RNAs and mRNAs between two groups were identified through fold-change filtering and Student's t-test."}, {"asset": "source:pmid:26484230", "locator": "sections[7] \"Normalization and data analysis\" paragraph 3", "quote": "Multiple testing corrections were performed by calculating the Benjamini-Hochberg false discovery rate (FDR)."}, {"asset": "source:pmid:26484230", "locator": "sections[5] \"Noncoding RNAs microarray data\" paragraph 2", "quote": "The SuperSeries is composed of three SubSeries as GSE56081 (lncRNA microarray), GSE63492 (miRNA microarray) and GSE67566 (circRNA microarray)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper used quantile normalization and Benjamini-Hochberg false discovery rate correction for statistical analysis of noncoding RNA and mRNA microarray data, with raw and annotated data accessible through GEO SuperSeries accession GSE67567.", "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:26484230"], "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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