RNA-seq data of soleus muscle tissue after spinal cord injury under conditions of inactivity and applied exercise.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32226812", "kind": "science-record", "revision": 8, "content_hash": "sha256:7a5c29831048ce421e92226f6239fc21bcbdb497a49faf1f056fa4b266bcc4b7", "created_at": "2026-11-01T15:40:58Z", "updated_at": "2026-11-01T22:44:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RNA-seq data of soleus muscle tissue after spinal cord injury under conditions of inactivity and applied exercise.", "doi": "10.1016/j.dib.2019.105056", "pmid": "32226812", "authors": ["Julia H Chariker", "Morgan Sharp", "Sujata Saraswat Ohri", "Cynthia Gomes", "Fiona Brabazon", "Kathryn A Harman", "Scott R Whittemore", "Jeffrey C Petruska", "David Sk Magnuson", "Eric C Rouchka"], "journal": "Data in brief", "year": 2020, "abstract": "Reduced muscle mass and increased fatiguability are major complications after spinal cord injury (SCI), and often hinder the rehabilitation efforts of patients. Such detriments to the musculoskeletal system, and the concomitant reduction in level of activity, contribute to secondary complications such as cardiovascular disease, diabetes, bladder dysfunction and liver damage. As a result of decreased weight-bearing capacity after SCI, muscles undergo morphological, metabolic, and contractile changes. Recent studies have shown that exercise after SCI decreases muscle wasting and reduces the burden of secondary complications. Here, we describe RNA sequencing data for detecting chronic transcriptomic changes in the rat soleus after SCI at two levels of injury severity, under conditions of restricted in-cage activity and two methods of applied exercise, swimming or shallow water walking. We demonstrate that the sequenced data are of good quality and show a high alignment rate to the Rattus norvegicus reference assembly (Rn6). The raw data, along with UCSC Genome Browser tracks created to facilitate exploration of gene expression, are available in the NCBI Gene Expression Omnibus (GEO; GSE129694).", "claims": [{"id": "claim-method", "statement": "Prior to examining gene expression, raw read counts were normalized to remove natural variation across samples arising from differences in tissue sampling and sequencing using DESeq2's default method, relative log expression (RLE) [[21], [22], [23]].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32226812", "locator": "sections[10] \"RNA-seq data analysis\" paragraph 4", "quote": "Prior to examining gene expression, raw read counts were normalized to remove natural variation across samples arising from differences in tissue sampling and sequencing using DESeq2's default method, relative log expression (RLE) [[21], [22], [23]]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw data and processed data can be accessed at NCBI's Gene Expression Omnibus (GEO accession GSE129694) http://identifiers.org/geo:GSE129694", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32226812", "locator": "sections[1] \"table-wrap\" paragraph 1", "quote": "Raw data and processed data can be accessed at NCBI's Gene Expression Omnibus (GEO accession GSE129694) http://identifiers.org/geo:GSE129694"}], "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:32226812"], "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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"section_title": "Data", "row_count": 21, "column_count": 7}, "table": {"label": "Table 1", "caption": "Sequencing and alignment summary.", "rows": [["Sample ID", "Experimental Group", "Input", "Number Uniquely Mapped Reads", "Percent Uniquely Mapped Reads", "Number Multi-mapped Reads", "Percent Multi-mapped Reads"], ["No SCI_Soleus, Rep. 1", "No SCI", "34,461,817", "30,234,805", "87.73%", "3,219,090", "9.34%"], ["No SCI_Soleus, Rep. 2", "No SCI", "52,659,350", "45,929,571", "87.22%", "5,330,524", "10.12%"], ["No SCI_Soleus, Rep. 3", "No SCI", "45,215,114", "39,486,401", "87.33%", "4,631,202", "10.24%"], ["No SCI_Soleus, Rep. 4", "No SCI", "43,282,634", "37,737,326", "87.19%", "4,403,769", "10.17%"], ["Contusion SCI_Soleus, Rep. 1", "CONT SCI", "29,674,153", "25,954,487", "87.46%", "3,064,891", "10.33%"], ["Contusion SCI_Soleus, Rep. 2", "CONT SCI", "31,390,027", "27,525,546", "87.69%", "3,175,265", "10.12%"], ["Contusion SCI_Soleus, Rep. 3", "CONT SCI", "33,185,693", "28,881,605", "87.03%", "3,477,562", "10.48%"], ["Contusion SCI_Soleus, Rep. 4", "CONT SCI", "49,832,639", "42,928,996", "86.15%", "5,210,955", "10.46%"], ["Contusion SCI + SWIM_Soleus, Rep. 1", "CONT SCI + SWIM", "36,938,790", "32,264,532", "87.35%", "3,802,398", "10.29%"], ["Contusion SCI + SWIM_Soleus, Rep. 2", "CONT SCI + SWIM", "28,309,521", "24,919,998", "88.03%", "2,781,084", "9.82%"], ["Contusion SCI + SWIM_Soleus, Rep. 3", "CONT SCI + SWIM", "29,319,512", "25,698,024", "87.65%", "2,953,908", "10.07%"], ["Contusion SCI + SWIM_Soleus, Rep. 4", "CONT SCI + SWIM", "41,954,615", "36,611,960", "87.27%", "4,268,234", "10.17%"], ["Contusion SCI + SWW_Soleus, Rep. 1", "CONT SCI + SWW", "29,577,126", "26,027,663", "88.00%", "2,942,085", "9.95%"], ["Contusion SCI + SWW_Soleus, Rep. 2", "CONT SCI + SWW", "30,996,221", "27,218,787", "87.81%", "3,104,595", "10.02%"], ["Contusion SCI + SWW_Soleus, Rep. 3", "CONT SCI + SWW", "28,425,718", "24,857,936", "87.45%", "2,928,521", "10.30%"], ["Contusion SCI + 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Here, we describe RNA sequencing data for detecting chronic transcriptomic ch", "be RNA sequencing data for detecting chronic transcriptomic changes in the rat soleus after SCI at two l"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["for detecting chronic transcriptomic changes in the rat soleus after SCI at two levels of injury sev", "ecting chronic transcriptomic changes in the rat soleus after SCI at two levels of injury sev", "tion for the exercises. Prior to injury, all rats were doubly-housed in standard cages and maintain", "t were available to all rats ad libitum. 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