{"id":"https://openalex.org/W3112286367","doi":"https://doi.org/10.1016/j.engreg.2020.12.002","title":"In silico analysis of RNA and small RNA sequencing data from human BM-MSCs and differentiated osteocytes, chondrocytes and tenocytes","display_name":"In silico analysis of RNA and small RNA sequencing data from human BM-MSCs and differentiated osteocytes, chondrocytes and tenocytes","publication_year":2020,"publication_date":"2020-12-08","ids":{"openalex":"https://openalex.org/W3112286367","doi":"https://doi.org/10.1016/j.engreg.2020.12.002","mag":"3112286367"},"language":"en","primary_location":{"id":"doi:10.1016/j.engreg.2020.12.002","doi":"https://doi.org/10.1016/j.engreg.2020.12.002","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.engreg.2020.12.002","pdf_url":"https://www.sciencedirect.com/science/article/pii/S2666138120300189/pdf","source":{"id":"https://openalex.org/S4210220692","display_name":"Engineered Regeneration","issn_l":"2666-1381","issn":["2666-1381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","poland-20"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Engineered Regeneration","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.sciencedirect.com/science/article/pii/S2666138120300189/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072425635","display_name":"Srinivas V. Koduru","orcid":"https://orcid.org/0000-0001-6827-2908","observed_orcids":["https://orcid.org/0000-0001-6827-2908"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]},{"id":"https://openalex.org/I82783531","display_name":"Penn State Milton S. Hershey Medical Center","ror":"https://ror.org/01h22ap11","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I82783531"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Srinivas V. Koduru","raw_affiliation_strings":["Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, United States","Department of Surgery, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, United States","Irvin S. Zubar Plastic Surgery Research Laboratory, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033-0850, United States"],"raw_orcid":"https://orcid.org/0000-0001-6827-2908","affiliations":[{"raw_affiliation_string":"Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, United States","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"Department of Surgery, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, United States","institution_ids":["https://openalex.org/I130769515","https://openalex.org/I82783531"]},{"raw_affiliation_string":"Irvin S. Zubar Plastic Surgery Research Laboratory, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033-0850, United States","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034108846","display_name":"Irina A. Elcheva","orcid":"https://orcid.org/0000-0002-3992-2817","observed_orcids":["https://orcid.org/0000-0002-3992-2817"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Irina A. Elcheva","raw_affiliation_strings":["Division of Pediatric Hematology/Oncology, Department of Pediatrics, Penn State College of Medicine, Hershey, PA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Pediatric Hematology/Oncology, Department of Pediatrics, Penn State College of Medicine, Hershey, PA, United States","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035651531","display_name":"Ashley N. Leberfinger","orcid":"https://orcid.org/0000-0002-8688-8789","observed_orcids":["https://orcid.org/0000-0002-8688-8789"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]},{"id":"https://openalex.org/I82783531","display_name":"Penn State Milton S. Hershey Medical Center","ror":"https://ror.org/01h22ap11","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I82783531"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ashley N. Leberfinger","raw_affiliation_strings":["Department of Surgery, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, United States","Irvin S. Zubar Plastic Surgery Research Laboratory, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033-0850, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, United States","institution_ids":["https://openalex.org/I130769515","https://openalex.org/I82783531"]},{"raw_affiliation_string":"Irvin S. Zubar Plastic Surgery Research Laboratory, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033-0850, United States","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056618662","display_name":"Dino J. Ravnic","orcid":"https://orcid.org/0000-0003-2261-5180","observed_orcids":["https://orcid.org/0000-0003-2261-5180"]},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]},{"id":"https://openalex.org/I82783531","display_name":"Penn State Milton S. Hershey Medical Center","ror":"https://ror.org/01h22ap11","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I82783531"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dino J. Ravnic","raw_affiliation_strings":["Department of Surgery, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, United States","Irvin S. Zubar Plastic Surgery Research Laboratory, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033-0850, United States"],"raw_orcid":"https://orcid.org/0000-0003-2261-5180","affiliations":[{"raw_affiliation_string":"Department of Surgery, Penn State Health Milton S. Hershey Medical Center, Hershey, PA, United States","institution_ids":["https://openalex.org/I130769515","https://openalex.org/I82783531"]},{"raw_affiliation_string":"Irvin S. Zubar Plastic Surgery Research Laboratory, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033-0850, United States","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5072425635"],"corresponding_institution_ids":["https://openalex.org/I130769515","https://openalex.org/I82783531"],"apc_list":{"value":700,"currency":"USD","value_usd":700},"apc_paid":{"value":700,"currency":"USD","value_usd":700},"fwci":0.5108,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.63653149,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"2","issue":null,"first_page":"19","last_page":"30"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10176","display_name":"Mesenchymal stem cell research","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2716","display_name":"Genetics (clinical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10176","display_name":"Mesenchymal stem cell research","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/2716","display_name":"Genetics (clinical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10105","display_name":"Osteoarthritis Treatment and Mechanisms","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10505","display_name":"Pluripotent Stem Cells Research","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bone-marrow-mesenchymal-stem-cells","display_name":"bone marrow mesenchymal stem cells","score":0.9110000133514404},{"id":"https://openalex.org/keywords/osteocytes","display_name":"osteocytes","score":0.6620000004768372},{"id":"https://openalex.org/keywords/chondrocytes","display_name":"chondrocytes","score":1.0},{"id":"https://openalex.org/keywords/tenocytes","display_name":"tenocytes","score":0.9959999918937683},{"id":"https://openalex.org/keywords/donor-age","display_name":"donor age","score":0.7910000085830688},{"id":"https://openalex.org/keywords/differentially-expressed-genes","display_name":"differentially expressed genes","score":0.9279999732971191},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.671999990940094},{"id":"https://openalex.org/keywords/mrna-expression","display_name":"mRNA expression","score":0.41499999165534973},{"id":"https://openalex.org/keywords/small-rna","display_name":"small RNA","score":0.6209999918937683},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"gene expression profiling","score":0.4880000054836273},{"id":"https://openalex.org/keywords/stem-cell-plasticity","display_name":"stem cell plasticity","score":0.7639999985694885},{"id":"https://openalex.org/keywords/engraftment","display_name":"engraftment","score":0.6520000100135803},{"id":"https://openalex.org/keywords/tissue-regeneration","display_name":"tissue regeneration","score":0.6179999709129333}],"concepts":[{"id":"https://openalex.org/C198826908","wikidata":"https://www.wikidata.org/wiki/Q1922379","display_name":"Mesenchymal stem cell","level":2,"score":0.8111450672149658},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6858228445053101},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.684028685092926},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.5800946950912476},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.562659740447998},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5611770153045654},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.5270878672599792},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.49498456716537476},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.49100902676582336},{"id":"https://openalex.org/C148738053","wikidata":"https://www.wikidata.org/wiki/Q210861","display_name":"Cellular differentiation","level":3,"score":0.4632934331893921},{"id":"https://openalex.org/C28328180","wikidata":"https://www.wikidata.org/wiki/Q48196","display_name":"Stem cell","level":2,"score":0.4201376438140869},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.4086226224899292},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32480424642562866}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1016/j.engreg.2020.12.002","doi":"https://doi.org/10.1016/j.engreg.2020.12.002","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.engreg.2020.12.002","pdf_url":"https://www.sciencedirect.com/science/article/pii/S2666138120300189/pdf","source":{"id":"https://openalex.org/S4210220692","display_name":"Engineered Regeneration","issn_l":"2666-1381","issn":["2666-1381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","poland-20"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Engineered Regeneration","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:b3a26199d2a04a04b023d3023ccd9704","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/b3a26199d2a04a04b023d3023ccd9704","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Engineered Regeneration, Vol 2, Iss , Pp 19-30 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1016/j.engreg.2020.12.002","doi":"https://doi.org/10.1016/j.engreg.2020.12.002","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.engreg.2020.12.002","pdf_url":"https://www.sciencedirect.com/science/article/pii/S2666138120300189/pdf","source":{"id":"https://openalex.org/S4210220692","display_name":"Engineered Regeneration","issn_l":"2666-1381","issn":["2666-1381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","poland-20"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Engineered Regeneration","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8371999859809875}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309370","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10"},{"id":"https://openalex.org/F4320310419","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231"},{"id":"https://openalex.org/F4320333195","display_name":"Penn State College of Medicine","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3112286367.pdf","grobid_xml":"https://content.openalex.org/works/W3112286367.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W30288693","https://openalex.org/W321346320","https://openalex.org/W1527969433","https://openalex.org/W1574963476","https://openalex.org/W1599031322","https://openalex.org/W1644840821","https://openalex.org/W1767988311","https://openalex.org/W1965172675","https://openalex.org/W1972801561","https://openalex.org/W1975403620","https://openalex.org/W1977907527","https://openalex.org/W1987003441","https://openalex.org/W1990363917","https://openalex.org/W1990792003","https://openalex.org/W1991964705","https://openalex.org/W1993483760","https://openalex.org/W2000944968","https://openalex.org/W2004977284","https://openalex.org/W2025240776","https://openalex.org/W2027141641","https://openalex.org/W2028011772","https://openalex.org/W2044193051","https://openalex.org/W2065831401","https://openalex.org/W2068439552","https://openalex.org/W2070054006","https://openalex.org/W2075876263","https://openalex.org/W2077327925","https://openalex.org/W2085662881","https://openalex.org/W2093142652","https://openalex.org/W2113619226","https://openalex.org/W2115662330","https://openalex.org/W2116041602","https://openalex.org/W2125684696","https://openalex.org/W2132803736","https://openalex.org/W2145769955","https://openalex.org/W2153263291","https://openalex.org/W2158804744","https://openalex.org/W2165697084","https://openalex.org/W2176312960","https://openalex.org/W2415876542","https://openalex.org/W2491494855","https://openalex.org/W2592259136","https://openalex.org/W2594458557","https://openalex.org/W2611044407","https://openalex.org/W2671688469","https://openalex.org/W2735348086","https://openalex.org/W2768781242","https://openalex.org/W2779409951","https://openalex.org/W2790396731","https://openalex.org/W2899279394","https://openalex.org/W2900964153","https://openalex.org/W3002549370","https://openalex.org/W7098463221"],"related_works":["https://openalex.org/W2155554926","https://openalex.org/W4393067584","https://openalex.org/W2517110431","https://openalex.org/W2062836285","https://openalex.org/W7116424554","https://openalex.org/W2111553416","https://openalex.org/W2080620471","https://openalex.org/W2912567789","https://openalex.org/W3158521459","https://openalex.org/W1965535285"],"abstract_inverted_index":{"Adult":[0],"stem":[1,29],"cells":[2,30],"have":[3,21],"a":[4,138,163,226],"remarkable":[5],"capacity":[6,228],"of":[7,27,40,48,74,115,141,167,202,205,220,229],"differentiating":[8],"into":[9],"various":[10],"cell":[11],"types":[12],"necessary":[13],"for":[14,200],"tissue":[15],"and":[16,42,67,76,82,87,99,113,117,125,158,174,207],"organ":[17],"regeneration.":[18],"Multiple":[19],"studies":[20],"focused":[22],"on":[23],"the":[24,37,134,217,233],"differentiation":[25,165],"potential":[26,166],"mesenchymal":[28],"(MSCs),":[31],"however":[32],"little":[33],"is":[34],"known":[35],"about":[36],"molecular":[38,218],"characteristics":[39],"MSCs":[41,75,168,230],"their":[43,77],"progenies":[44],"obtained":[45,60],"from":[46,61,96,170,187],"donors":[47,73],"different":[49],"ages.":[50],"In":[51,209],"this":[52],"study,":[53],"we":[54],"analyzed":[55,101,147],"publicly":[56],"available":[57],"sequencing":[58,92],"data":[59,93,199,212],"young":[62,135],"(~22-year-old,":[63],"n":[64,70],"=":[65,71],"8)":[66,72],"older":[68,118,159],"(~65.5-year-old,":[69],"differentiated":[78,189],"counterparts:":[79],"osteocytes,":[80,111],"chondrocytes":[81,112],"tenocytes.":[83],"The":[84],"raw":[85],"mRNA":[86,175],"small":[88],"RNA":[89],"(non-coding":[90],"RNA)":[91],"was":[94],"downloaded":[95],"NIH":[97],"BioProjects":[98],"systematically":[100],"in":[102,109,130,145,152,184,236],"order":[103],"to":[104,196,231],"identify":[105],"uniquely":[106],"expressed":[107,143],"genes":[108,127,144],"MSC-derived":[110,148],"tenocytes":[114],"younger":[116,157,171],"people.":[119,238],"We":[120],"identified":[121],"many":[122],"commonly":[123],"up-":[124],"downregulated":[126],"are":[128],"similar":[129],"both":[131,185],"groups.":[132],"However,":[133],"group":[136],"displayed":[137],"greater":[139,164],"variety":[140],"differentially":[142],"all":[146,188],"cells.":[149],"This":[150],"discrepancy":[151],"gene":[153],"expression":[154],"profiles":[155],"between":[156],"groups":[160,186],"may":[161,213],"indicate":[162],"isolated":[169],"donors.":[172],"miRNA":[173],"integrated":[176],"analysis":[177,192],"showed":[178],"key":[179],"miRNAs":[180],"that":[181],"regulate":[182],"mRNAs":[183],"lineages.":[190],"Our":[191],"provides":[193],"additional":[194],"information":[195],"previously":[197],"reported":[198],"identification":[201],"MSC":[203],"markers":[204],"plasticity":[206],"engraftment.":[208],"addition,":[210],"our":[211],"shed":[214],"light":[215],"upon":[216],"mechanisms":[219],"age-associated":[221],"musculoskeletal":[222],"diseases":[223],"caused":[224],"by":[225],"decreased":[227],"regenerate":[232],"locomotor":[234],"system":[235],"elderly":[237]},"counts_by_year":[{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2020-12-21T00:00:00"}