mRNA and microRNA transcriptomics analyses in a murine model of dystrophin loss and therapeutic restoration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26981371", "kind": "science-record", "revision": 7, "content_hash": "sha256:5d934d1eaa25129640202739bb54bafd4c581e8726776682cf6848caf1752d44", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T21:58:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "mRNA and microRNA transcriptomics analyses in a murine model of dystrophin loss and therapeutic restoration.", "doi": "10.1016/j.gdata.2015.11.025", "pmid": "26981371", "authors": ["Thomas C Roberts", "K Emelie M Blomberg", "C I Edvard Smith", "Samir El Andaloussi", "Matthew J A Wood"], "journal": "Genomics data", "year": 2016, "abstract": "Duchenne muscular dystrophy (DMD) is a pediatric, X-linked, progressive muscle-wasting disorder caused by loss of function mutations affecting the gene encoding the dystrophin protein. While the primary genetic insult in DMD is well described, many details of the molecular and cellular pathologies that follow dystrophin loss are incompletely understood. To investigate gene expression in dystrophic muscle we have applied mRNA and microRNA (miRNA) microarray technology to the mdx mouse model of DMD. This study was designed to generate a complete description of gene expression changes associated with dystrophic pathology and the response to an experimental therapy which restores dystrophin protein function. These datasets have enabled (1) the determination of gene expression changes associated with dystrophic pathology, (2) identification of differentially expressed genes that are restored towards wild-type levels after therapeutic dystrophin rescue, (3) investigation of the correlation between mRNA and protein expression (determined by parallel mass spectrometry proteomics analysis), and (4) prediction of pathology associated miRNA-target interactions. Here we describe in detail how the data were generated including the basic analysis as contained in the manuscript published in Human Molecular Genetics with PMID 26385637. The data have been deposited in the Gene Expression Omnibus (GEO) with the accession number GSE64420.", "claims": [{"id": "claim-method", "statement": "Unpaired 2-sided Student's t-test was performed with the criterion for differentially expressed transcripts set to P < 0.05. The microarray data discussed in this study have been deposited in NCBI's Gene Expression Omnibus (3) and are accessible through GEO Series accession number GSE64420 (mRNA data: GSE64418, miRNA data: GSE64419).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981371", "locator": "sections[7] \"mRNA and miRNA microarray processing and statistical analysis\" paragraph 3", "quote": "Unpaired 2-sided Student's t-test was performed with the criterion for differentially expressed transcripts set to P < 0.05."}, {"asset": "source:pmid:26981371", "locator": "sections[7] \"mRNA and miRNA microarray processing and statistical analysis\" paragraph 5", "quote": "The microarray data discussed in this study have been deposited in NCBI's Gene Expression Omnibus (3) and are accessible through GEO Series accession number GSE64420 (mRNA data: GSE64418, miRNA data: GSE64419)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data discussed in this study have been deposited in NCBI's Gene Expression Omnibus (3) and are accessible through GEO Series accession number GSE64420 (mRNA data: GSE64418, miRNA data: GSE64419).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26981371", "locator": "sections[7] \"mRNA and miRNA microarray processing and statistical analysis\" paragraph 5", "quote": "The microarray data discussed in this study have been deposited in NCBI's Gene Expression Omnibus (3) and are accessible through GEO Series accession number GSE64420 (mRNA data: GSE64418, miRNA data: GSE64419)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used an unpaired two-sided Student's t-test with P < 0.05 and false-discovery-rate q values to identify differential expression, and deposited its source data in GEO under accession GSE64420 (mRNA: GSE64418; miRNA: GSE64419).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Unpaired 2-sided Student's t-test was performed with the criterion for differentially expressed transcripts set to P < 0.05."}, "evidence": [{"asset": "source:pmid:26981371", "locator": "sections[7] \"mRNA and miRNA microarray processing and statistical analysis\" paragraph 3", "quote": "Unpaired 2-sided Student's t-test was performed with the criterion for differentially expressed transcripts set to P < 0.05."}, {"asset": "source:pmid:26981371", "locator": "sections[7] \"mRNA and miRNA microarray processing and statistical analysis\" paragraph 3", "quote": "False Discovery Rate (FDR) estimations were performed by calculating q values (qvalue R package) from the P-value lists."}, {"asset": "source:pmid:26981371", "locator": "sections[7] \"mRNA and miRNA microarray processing and statistical analysis\" paragraph 5", "quote": "The microarray data discussed in this study have been deposited in NCBI's Gene Expression Omnibus (3) and are accessible through GEO Series accession number GSE64420 (mRNA data: GSE64418, miRNA data: GSE64419)."}, {"asset": "source:pmid:26981371", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data have been deposited in the Gene Expression Omnibus (GEO) with the accession number GSE64420."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study used an unpaired two-sided Student's t-test with P < 0.05 and false-discovery-rate q values to identify differential expression, and deposited its source data in GEO under accession GSE64420 (mRNA: GSE64418; miRNA: GSE64419).", "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:26981371"], "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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This study was designed to generate", "RNA (miRNA) microarray technology to the mdx mouse model of DMD. This study was designed to gen", "by MALDI-TOF MS as described previously [1]. Mice were sacrificed by escalating CO2 concentration and death co"], "order_basis": "paper_text_order:3", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["le we have applied mRNA and microRNA (miRNA) microarray technology to the mdx mouse model of DMD. Th", "°C until ready for analysis. mRNA and miRNA microarray processing and statistical analysis Labeling", "82 probe sets remained after filtering). 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