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This progressive RGC death is considered to originate in axonal injury caused by compression of the axon bundles in the ONH. However, the molecular pathomechanisms of axonal injury-induced RGC death are not yet well understood. Here, we used RNA sequencing (RNA-seq) to examine transcriptome changes in rat retinas 2 days after optic nerve transection (ONT) and then used computational techniques to predict the resulting alterations in the transcriptional regulatory network. RNA-seq revealed 267 differentially expressed genes after ONT, 218 of which were annotated and 49 unannotated. We also identified differentially expressed transcripts, including potentially novel isoforms. An<jats:italic>in silico<\/jats:italic>pathway analysis predicted that CREB1 was the most significant upstream regulator. Thus, this study identified genes and pathways that may be involved in the pathomechanisms of axonal injury. We believe that our data should serve as a valuable resource to understand the molecular processes that define axonal injury-driven RGC death and to discover novel therapeutic targets for glaucoma.<\/jats:p>","DOI":"10.1038\/srep28736","type":"journal-article","created":{"date-parts":[[2016,6,29]],"date-time":"2016-06-29T10:07:43Z","timestamp":1467194863000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":39,"title":["Transcriptome profiling of the rat retina after optic nerve transection"],"prefix":"10.1038","volume":"6","author":[{"given":"Masayuki","family":"Yasuda","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuji","family":"Tanaka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kazuko","family":"Omodaka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Koji M.","family":"Nishiguchi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Orie","family":"Nakamura","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Satoru","family":"Tsuda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Toru","family":"Nakazawa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,6,29]]},"reference":[{"key":"BFsrep28736_CR1","doi-asserted-by":"crossref","first-page":"2081","DOI":"10.1016\/j.ophtha.2014.05.013","volume":"121","author":"Y-C Tham","year":"2014","unstructured":"Tham, Y.-C. et al. Global prevalence of glaucoma and projections of glaucoma burden through 2040: a systematic review and meta-analysis. Ophthalmology 121, 2081\u20132090 (2014).","journal-title":"Ophthalmology"},{"key":"BFsrep28736_CR2","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1056\/NEJMra0804630","volume":"360","author":"YH Kwon","year":"2009","unstructured":"Kwon, Y. H., Fingert, J. H., Kuehn, M. H. & Alward, W. L. Primary open-angle glaucoma. N. Engl. J. Med. 360, 1113\u20131124 (2009).","journal-title":"N. Engl. J. Med."},{"key":"BFsrep28736_CR3","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1001\/archopht.120.10.1268","volume":"120","author":"A Heijl","year":"2002","unstructured":"Heijl, A. et al. Reduction of intraocular pressure and glaucoma progression: results from the Early Manifest Glaucoma Trial. Arch. Ophthalmol. 120, 1268\u20131279 (2002).","journal-title":"Arch. 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