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In this study, we simultaneously interrogate the expression profiles of lncRNAs, miRNAs, and mRNAs changes during focal ischemia induced by transient middle cerebral artery occlusion. A set of 1924 novel lncRNAs were identified and may involve brain injury and DNA repair as revealed by coexpression network analysis. Furthermore, many short interspersed elements (SINE) mediated lncRNA:mRNA duplexes were identified, implying that lncRNAs mediate Staufen1-mediated mRNA decay (SMD) which may play a role during focal ischemia. Moreover, based on the competitive endogenous RNA (ceRNA) hypothesis, a stroke regulatory ceRNA network which reveals functional lncRNA:miRNA:mRNA interactions was revealed in ischemic stroke. In brief, this work reports a large number of novel lncRNAs responding to focal ischemia and constructs a systematic RNA regulation network which highlighted the role of ncRNAs in ischemic stroke.<\/jats:p>","DOI":"10.1155\/2018\/8354350","type":"journal-article","created":{"date-parts":[[2018,1,8]],"date-time":"2018-01-08T18:35:06Z","timestamp":1515436506000},"page":"1-13","source":"Crossref","is-referenced-by-count":14,"title":["Systematic Analysis of RNA Regulatory Network in Rat Brain after Ischemic Stroke"],"prefix":"10.1155","volume":"2018","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4459-9348","authenticated-orcid":true,"given":"Juan","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People\u2019s Hospital, Shanghai, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kun-shan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Stem Cell Translational 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