{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T21:45:41Z","timestamp":1788385541460,"version":"build-2803163510"},"update-to":[{"DOI":"10.1371\/journal.pgen.1011879","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T00:00:00Z","timestamp":1758672000000}}],"reference-count":135,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T00:00:00Z","timestamp":1758240000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100001209","name":"Knights Templar Eye Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001209","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008562","name":"University of Texas at Austin","doi-asserted-by":"publisher","award":["None"],"award-info":[{"award-number":["None"]}],"id":[{"id":"10.13039\/100008562","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>Retinal ganglion cells (RGCs) are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma, optic neuropathies and after ocular trauma results in irreversible loss of vision as RGCs do not regenerate in the human eye. Moreover, there are no FDA approved therapies that prevent RGC death and\/or promote RGC survival in the diseased or injured eye. There is a critical need to better understand the molecular underpinnings of neuroprotection to develop effective therapeutic approaches to preserve damaged RGCs. Unlike in mammals, RGCs in zebrafish are resilient to optic nerve injury, even after complete transection of the optic nerve. Here, we leveraged this unique model and utilized single-cell RNA sequencing to characterize RGC responses to injury and identify putative neuroprotective and regenerative pathways. RGCs are heterogeneous and studies in mice have shown that there is differential resiliency across RGC subtypes. Our results demonstrated that all RGC subtypes are resilient to injury in zebrafish. Quantifying changes in gene expression revealed the upregulation of progenitor and regenerative markers in all RGC subtypes after injury as well as distinct early and late phases to the injury response. This shift in gene expression causes injury-responsive RGCs to resemble RGC subtype 3, a low frequency population of endogenous immature RGCs that are normally maintained in the wild-type, uninjured adult retina. A similar but restricted transcriptomic injury response in RGCs of the uninjured contralateral eye was also detected, highlighting a systemic RGC response to unilateral optic nerve injury. Taken together, these results demonstrate that zebrafish RGCs dedifferentiate in response to injury, and this may be a novel mechanism mediating their unique cell survival and regenerative capabilities.<\/jats:p>","DOI":"10.1371\/journal.pgen.1011879","type":"journal-article","created":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T21:25:23Z","timestamp":1758317123000},"page":"e1011879","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Zebrafish optic nerve injury results in systemic retinal ganglion cell dedifferentiation"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0979-1809","authenticated-orcid":true,"given":"Ashrifa","family":"Ali","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9459-5548","authenticated-orcid":true,"given":"Hannah","family":"Schriever","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dennis","family":"Kostka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8398-3131","authenticated-orcid":true,"given":"Takaaki","family":"Kuwajima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6093-2262","authenticated-orcid":true,"given":"Kristen M.","family":"Koenig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9422-6312","authenticated-orcid":true,"given":"Jeffrey M.","family":"Gross","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,9,19]]},"reference":[{"key":"pgen.1011879.ref001","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1186\/s13024-023-00655-y","article-title":"Retinal ganglion cell repopulation for vision restoration in optic neuropathy: a roadmap from the RReSTORe Consortium","volume":"18","author":"JR Soucy","year":"2023","journal-title":"Molecular Neurodegeneration"},{"issue":"16","key":"pgen.1011879.ref002","doi-asserted-by":"crossref","DOI":"10.1016\/j.neuron.2022.06.002","article-title":"Overlapping transcriptional programs promote survival and axonal regeneration of injured retinal ganglion cells","volume":"110","author":"A Jacobi","year":"2022","journal-title":"Neuron"},{"key":"pgen.1011879.ref003","doi-asserted-by":"crossref","first-page":"102428","DOI":"10.1016\/j.coph.2023.102428","article-title":"Optic nerve regeneration: Potential treatment approaches","volume":"74","author":"J Lee","year":"2024","journal-title":"Curr Opin Pharmacol"},{"issue":"6","key":"pgen.1011879.ref004","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1111\/ceo.14259","article-title":"Optic nerve diseases and regeneration: How far are we from the promised land?","volume":"51","author":"L-P Cen","year":"2023","journal-title":"Clin Exp Ophthalmol"},{"key":"pgen.1011879.ref005","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1146\/annurev-vision-022720-094953","article-title":"Axon Regeneration in the Mammalian Optic Nerve","volume":"6","author":"PR Williams","year":"2020","journal-title":"Annu Rev Vis Sci"},{"key":"pgen.1011879.ref006","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1016\/B978-0-12-384878-9.00007-8","article-title":"Toward a better understanding of human eye disease insights from the zebrafish, Danio rerio","volume":"100","author":"J Bibliowicz","year":"2011","journal-title":"Prog Mol Biol Transl Sci"},{"key":"pgen.1011879.ref007","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1146\/annurev-vision-082114-035717","article-title":"Zebrafish Models of Retinal Disease","volume":"1","author":"BA Link","year":"2015","journal-title":"Annu Rev Vis Sci"},{"key":"pgen.1011879.ref008","doi-asserted-by":"crossref","first-page":"118","DOI":"10.3389\/fncel.2015.00118","article-title":"Characterization of optic nerve regeneration using transgenic zebrafish","volume":"9","author":"H Diekmann","year":"2015","journal-title":"Front Cell Neurosci"},{"key":"pgen.1011879.ref009","first-page":"21","volume-title":"Functional regeneration and remyelination in the zebrafish optic nerve. Neural Regeneration","author":"SQ Zou","year":"2015"},{"issue":"2","key":"pgen.1011879.ref010","article-title":"Neurogenesis of retinal ganglion cells is not essential to visual functional recovery after optic nerve injury in adult zebrafish","volume":"8","author":"S Zou","year":"2013","journal-title":"PLoS One"},{"key":"pgen.1011879.ref011","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.preteyeres.2011.11.002","article-title":"The molecular basis of retinal ganglion cell death in glaucoma","volume":"31","author":"M Almasieh","year":"2012","journal-title":"Prog Retin Eye Res"},{"key":"pgen.1011879.ref012","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1016\/j.ophtha.2011.11.003","article-title":"Glaucoma 2.0: neuroprotection, neuroregeneration, neuroenhancement","volume":"119","author":"EE Chang","year":"2012","journal-title":"Ophthalmology"},{"key":"pgen.1011879.ref013","doi-asserted-by":"crossref","first-page":"100769","DOI":"10.1016\/j.preteyeres.2019.07.002","article-title":"Axon injury signaling and compartmentalized injury response in glaucoma","volume":"73","author":"SB Syc-Mazurek","year":"2019","journal-title":"Prog Retin Eye Res"},{"issue":"8","key":"pgen.1011879.ref014","doi-asserted-by":"crossref","DOI":"10.1242\/dev.199694","article-title":"Retinal ganglion cell survival after severe optic nerve injury is modulated by crosstalk between Jak\/Stat signaling and innate immune responses in the zebrafish retina","volume":"149","author":"S Chen","year":"2022","journal-title":"Development"},{"issue":"2","key":"pgen.1011879.ref015","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1016\/j.ydbio.2007.09.019","article-title":"Gene expression analysis of zebrafish retinal ganglion cells during optic nerve regeneration identifies KLF6a and KLF7a as important regulators of axon regeneration","volume":"312","author":"MB Veldman","year":"2007","journal-title":"Dev Biol"},{"issue":"7","key":"pgen.1011879.ref016","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1523\/JNEUROSCI.3898-13.2014","article-title":"Jak\/Stat signaling stimulates zebrafish optic nerve regeneration and overcomes the inhibitory actions of Socs3 and Sfpq","volume":"34","author":"F Elsaeidi","year":"2014","journal-title":"J Neurosci"},{"issue":"3","key":"pgen.1011879.ref017","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0093258","article-title":"RNA sequence reveals mouse retinal transcriptome changes early after axonal injury","volume":"9","author":"M Yasuda","year":"2014","journal-title":"PLoS One"},{"key":"pgen.1011879.ref018","doi-asserted-by":"crossref","first-page":"28736","DOI":"10.1038\/srep28736","article-title":"Transcriptome profiling of the rat retina after optic nerve transection","volume":"6","author":"M Yasuda","year":"2016","journal-title":"Sci Rep"},{"key":"pgen.1011879.ref019","first-page":"1050","article-title":"Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush","volume":"14","author":"M Agudo","year":"2008","journal-title":"Molecular Vision"},{"issue":"3","key":"pgen.1011879.ref020","doi-asserted-by":"crossref","first-page":"633","DOI":"10.3390\/cells10030633","article-title":"Neurodegeneration, Neuroprotection and Regeneration in the Zebrafish Retina","volume":"10","author":"Jr Stella SL","year":"2021","journal-title":"Cells"},{"issue":"1","key":"pgen.1011879.ref021","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1038\/s41467-018-05134-3","article-title":"Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes","volume":"9","author":"BA Rheaume","year":"2018","journal-title":"Nat Commun"},{"issue":"5","key":"pgen.1011879.ref022","article-title":"Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina","volume":"176","author":"Y-R Peng","year":"2019","journal-title":"Cell"},{"issue":"18","key":"pgen.1011879.ref023","doi-asserted-by":"crossref","DOI":"10.15252\/embj.2018100811","article-title":"A single-cell transcriptome atlas of the adult human retina","volume":"38","author":"SW Lukowski","year":"2019","journal-title":"EMBO J"},{"key":"pgen.1011879.ref024","doi-asserted-by":"crossref","first-page":"9802","DOI":"10.1038\/s41598-020-66092-9","article-title":"Cell Atlas of the Human Fovea and Peripheral Retina","volume":"10","author":"W Yan","year":"2020","journal-title":"Sci Rep"},{"issue":"4","key":"pgen.1011879.ref025","doi-asserted-by":"crossref","DOI":"10.1016\/j.neuron.2020.12.003","article-title":"Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior","volume":"109","author":"Y K\u00f6lsch","year":"2021","journal-title":"Neuron"},{"issue":"6","key":"pgen.1011879.ref026","article-title":"Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes","volume":"104","author":"NM Tran","year":"2019","journal-title":"Neuron"},{"key":"pgen.1011879.ref027","doi-asserted-by":"crossref","DOI":"10.1242\/dev.201644","article-title":"Pten inhibition dedifferentiates long-distance axon-regenerating intrinsically photosensitive retinal ganglion cells and upregulates mitochondria-associated Dynlt1a and Lars2","volume":"150","author":"BA Rheaume","year":"2023","journal-title":"Development"},{"issue":"4","key":"pgen.1011879.ref028","doi-asserted-by":"crossref","first-page":"3253","DOI":"10.3390\/ijms24043253","article-title":"Specific Activation of Yamanaka Factors via HSF1 Signaling in the Early Stage of Zebrafish Optic Nerve Regeneration","volume":"24","author":"K Sugitani","year":"2023","journal-title":"Int J Mol Sci"},{"issue":"8","key":"pgen.1011879.ref029","doi-asserted-by":"crossref","first-page":"888","DOI":"10.1016\/j.neuint.2011.02.017","article-title":"HSP70, the earliest-induced gene in the zebrafish retina during optic nerve regeneration: its role in cell survival","volume":"58","author":"M Nagashima","year":"2011","journal-title":"Neurochem Int"},{"issue":"1","key":"pgen.1011879.ref030","doi-asserted-by":"crossref","first-page":"14198","DOI":"10.1038\/s41598-019-50485-6","article-title":"Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors","volume":"9","author":"SP Dhara","year":"2019","journal-title":"Sci Rep"},{"key":"pgen.1011879.ref031","doi-asserted-by":"crossref","first-page":"109","DOI":"10.3389\/fncel.2020.00109","article-title":"Longitudinal Morphological and Functional Assessment of RGC Neurodegeneration After Optic Nerve Crush in Mouse","volume":"14","author":"L Li","year":"2020","journal-title":"Front Cell Neurosci"},{"key":"pgen.1011879.ref032","doi-asserted-by":"crossref","first-page":"19126","DOI":"10.1073\/pnas.0709337104","article-title":"OFF ganglion cells cannot drive the optokinetic reflex in zebrafish","volume":"104","author":"F Emran","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"15","key":"pgen.1011879.ref033","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2020.05.055","article-title":"Zebrafish Retinal Ganglion Cells Asymmetrically Encode Spectral and Temporal Information across Visual Space","volume":"30","author":"M Zhou","year":"2020","journal-title":"Curr Biol"},{"issue":"4","key":"pgen.1011879.ref034","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1038\/aps.2009.24","article-title":"Molecular mechanisms of excitotoxicity and their relevance to pathogenesis of neurodegenerative diseases","volume":"30","author":"X Dong","year":"2009","journal-title":"Acta Pharmacol Sin"},{"key":"pgen.1011879.ref035","doi-asserted-by":"crossref","first-page":"24851","DOI":"10.1038\/srep24851","article-title":"Zebrafish M\u00fcller glia-derived progenitors are multipotent, exhibit proliferative biases and regenerate excess neurons","volume":"6","author":"C Powell","year":"2016","journal-title":"Sci Rep"},{"issue":"4","key":"pgen.1011879.ref036","doi-asserted-by":"crossref","first-page":"733","DOI":"10.24272\/j.issn.2095-8137.2025.020","article-title":"From injury to recovery: Spatiotemporal dynamics of the visual pathway during spontaneous structural and functional regeneration after optic nerve transection in zebrafish","volume":"46","author":"B-G Shen","year":"2025","journal-title":"Zool Res"},{"issue":"2","key":"pgen.1011879.ref037","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/s41587-021-01033-z","article-title":"Differential abundance testing on single-cell data using k-nearest neighbor graphs","volume":"40","author":"E Dann","year":"2022","journal-title":"Nat Biotechnol"},{"issue":"23","key":"pgen.1011879.ref038","doi-asserted-by":"crossref","first-page":"15416","DOI":"10.3390\/ijms232315416","article-title":"Role of the Intermediate Filament Protein Peripherin in Health and Disease","volume":"23","author":"R Romano","year":"2022","journal-title":"Int J Mol Sci"},{"key":"pgen.1011879.ref039","doi-asserted-by":"crossref","first-page":"633","DOI":"10.3389\/fgene.2018.00633","article-title":"Different Effect of Sox11 in Retinal Ganglion Cells Survival and Axon Regeneration","volume":"9","author":"Y Li","year":"2018","journal-title":"Front Genet"},{"key":"pgen.1011879.ref040","doi-asserted-by":"crossref","DOI":"10.1016\/j.neuron.2017.05.035","article-title":"Sox11 expression promotes regeneration of some retinal ganglion cell types but kills others","volume":"94","author":"M Norsworthy","year":"2017","journal-title":"Neuron"},{"issue":"1","key":"pgen.1011879.ref041","article-title":"Posttranslational Modification of Sox11 Regulates RGC Survival and Axon Regeneration","volume":"8","author":"K-C Chang","year":"2021","journal-title":"eNeuro"},{"issue":"9","key":"pgen.1011879.ref042","doi-asserted-by":"crossref","first-page":"4417","DOI":"10.1007\/s00018-021-03814-w","article-title":"Genetic control of retinal ganglion cell genesis","volume":"78","author":"J Lyu","year":"2021","journal-title":"Cell Mol Life Sci"},{"issue":"6","key":"pgen.1011879.ref043","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1002\/stem.2812","article-title":"Human Periodontal Ligament-Derived Stem Cells Promote Retinal Ganglion Cell Survival and Axon Regeneration After Optic Nerve Injury","volume":"36","author":"L-P Cen","year":"2018","journal-title":"Stem Cells"},{"key":"pgen.1011879.ref044","doi-asserted-by":"crossref","first-page":"108587","DOI":"10.1016\/j.exer.2021.108587","article-title":"Kr\u00fcppel-like factor 7 protects retinal ganglion cells and promotes functional preservation via activating the Akt pathway after retinal ischemia-reperfusion injury","volume":"207","author":"Z Li","year":"2021","journal-title":"Exp Eye Res"},{"issue":"14","key":"pgen.1011879.ref045","article-title":"Mycb and Mych stimulate M\u00fcller glial cell reprogramming and proliferation in the uninjured and injured zebrafish retina","volume":"151","author":"M-S Lee","year":"2024","journal-title":"Development"},{"issue":"10","key":"pgen.1011879.ref046","doi-asserted-by":"crossref","first-page":"1426","DOI":"10.1038\/s41556-023-01234-5","article-title":"Myc-dependent dedifferentiation of Gata6+ epidermal cells resembles reversal of terminal differentiation","volume":"25","author":"M Bernab\u00e9-Rubio","year":"2023","journal-title":"Nat Cell Biol"},{"issue":"3","key":"pgen.1011879.ref047","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.neures.2008.03.008","article-title":"Changes of phospho-growth-associated protein 43 (phospho-GAP43) in the zebrafish retina after optic nerve injury: a long-term observation","volume":"61","author":"M Kaneda","year":"2008","journal-title":"Neurosci Res"},{"key":"pgen.1011879.ref048","article-title":"Mapping single-cell developmental potential in health and disease with interpretable deep learning","author":"M Kang","year":"2024","journal-title":"bioRxiv"},{"issue":"7745","key":"pgen.1011879.ref049","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1038\/s41586-019-0969-x","article-title":"The single-cell transcriptional landscape of mammalian organogenesis","volume":"566","author":"J Cao","year":"2019","journal-title":"Nature"},{"issue":"17","key":"pgen.1011879.ref050","doi-asserted-by":"crossref","first-page":"10179","DOI":"10.3390\/ijms231710179","article-title":"Retinal Ganglion Cell Survival and Axon Regeneration after Optic Nerve Injury: Role of Inflammation and Other Factors","volume":"23","author":"KA Wong","year":"2022","journal-title":"Int J Mol Sci"},{"key":"pgen.1011879.ref051","doi-asserted-by":"crossref","first-page":"860070","DOI":"10.3389\/fimmu.2022.860070","article-title":"Neuroinflammation, Microglia and Implications for Retinal Ganglion Cell Survival and Axon Regeneration in Traumatic Optic Neuropathy","volume":"13","author":"NPB Au","year":"2022","journal-title":"Front Immunol"},{"key":"pgen.1011879.ref052","doi-asserted-by":"crossref","first-page":"5767","DOI":"10.1038\/s41598-021-85181-x","article-title":"Characterization of the role of autophagy in retinal ganglion cell survival over time using a rat model of chronic ocular hypertension","volume":"11","author":"SH Lee","year":"2021","journal-title":"Sci Rep"},{"issue":"1","key":"pgen.1011879.ref053","doi-asserted-by":"crossref","first-page":"13321","DOI":"10.1038\/s41598-018-30165-7","article-title":"Different contributions of autophagy to retinal ganglion cell death in the diabetic and glaucomatous retinas","volume":"8","author":"H-YL Park","year":"2018","journal-title":"Sci Rep"},{"issue":"7","key":"pgen.1011879.ref054","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1007\/s12264-020-00490-x","article-title":"Altered Energy Metabolism During Early Optic Nerve Crush Injury: Implications of Warburg-Like Aerobic Glycolysis in Facilitating Retinal Ganglion Cell Survival","volume":"36","author":"J Zhu","year":"2020","journal-title":"Neurosci Bull"},{"issue":"1","key":"pgen.1011879.ref055","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/cdd.2011.88","article-title":"Autophagy promotes survival of retinal ganglion cells after optic nerve axotomy in mice","volume":"19","author":"N Rodr\u00edguez-Muela","year":"2012","journal-title":"Cell Death Differ"},{"key":"pgen.1011879.ref056","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1007\/s12031-016-0728-5","article-title":"Mitochondrial uncoupling protein 2 (UCP2) regulates retinal ganglion cell number and survival","volume":"58","author":"CJ Barnstable","year":"2016","journal-title":"J Mol Neurosci"},{"key":"pgen.1011879.ref057","doi-asserted-by":"crossref","DOI":"10.1038\/cddis.2017.212","article-title":"Damage-induced neuronal endopeptidase (DINE) enhances axonal regeneration potential of retinal ganglion cells after optic nerve injury","volume":"8","author":"A Kaneko","year":"2017","journal-title":"Cell Death Dis"},{"key":"pgen.1011879.ref058","article-title":"Suppressing DNMT3a Alleviates the Intrinsic Epigenetic Barrier for Optic Nerve Regeneration and Restores Vision in Adult Mice","author":"WL Tai","year":"2023","journal-title":"bioRxiv"},{"issue":"1","key":"pgen.1011879.ref059","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s42003-023-04463-4","article-title":"Purified regenerating retinal neurons reveal regulatory role of DNA methylation-mediated Na+\/K+-ATPase in murine axon regeneration","volume":"6","author":"E Rizk","year":"2023","journal-title":"Commun Biol"},{"issue":"6","key":"pgen.1011879.ref060","doi-asserted-by":"crossref","first-page":"100298","DOI":"10.1016\/j.xgen.2023.100298","article-title":"A multi-omics atlas of the human retina at single-cell resolution","volume":"3","author":"Q Liang","year":"2023","journal-title":"Cell Genom"},{"issue":"2","key":"pgen.1011879.ref061","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1002\/cne.10323","article-title":"Large-scale morphological survey of mouse retinal ganglion cells","volume":"451","author":"W Sun","year":"2002","journal-title":"J Comp Neurol"},{"key":"pgen.1011879.ref062","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/nn.3032","article-title":"Transcriptional code and disease map for adult retinal cell types","volume":"15","author":"S Siegert","year":"2012","journal-title":"Nat Neurosci"},{"issue":"21","key":"pgen.1011879.ref063","doi-asserted-by":"crossref","first-page":"7753","DOI":"10.1523\/JNEUROSCI.0907-11.2011","article-title":"Retinal ganglion cells with distinct directional preferences differ in molecular identity, structure, and central projections","volume":"31","author":"JN Kay","year":"2011","journal-title":"J Neurosci"},{"issue":"7586","key":"pgen.1011879.ref064","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nature16468","article-title":"The functional diversity of retinal ganglion cells in the mouse","volume":"529","author":"T Baden","year":"2016","journal-title":"Nature"},{"issue":"11","key":"pgen.1011879.ref065","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1167\/tvst.9.11.14","article-title":"Probing ON and OFF Retinal Pathways in Glaucoma Using Electroretinography","volume":"9","author":"AW Kong","year":"2020","journal-title":"Transl Vis Sci Technol"},{"key":"pgen.1011879.ref066","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.neuroscience.2018.07.040","article-title":"Selective Vulnerability of \u03b1OFF Retinal Ganglion Cells during Onset of Autoimmune Optic Neuritis","volume":"393","author":"C Mayer","year":"2018","journal-title":"Neuroscience"},{"key":"pgen.1011879.ref067","doi-asserted-by":"crossref","first-page":"905352","DOI":"10.3389\/fopht.2022.905352","article-title":"Differential retinal ganglion cell vulnerability, a critical clue for the identification of neuroprotective genes in glaucoma","volume":"2","author":"D Amin","year":"2022","journal-title":"Front Ophthalmol"},{"key":"pgen.1011879.ref068","doi-asserted-by":"crossref","first-page":"956279","DOI":"10.3389\/fcell.2022.956279","article-title":"Subtype-specific survival and regeneration of retinal ganglion cells in response to injury","volume":"10","author":"ML Tapia","year":"2022","journal-title":"Front Cell Dev Biol"},{"key":"pgen.1011879.ref069","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/978-1-0716-4140-8_16","article-title":"Retinal ganglion cell subtypes and their vulnerability in glaucoma","volume":"2858","author":"JE Morgan","year":"2025","journal-title":"Methods Mol Biol"},{"issue":"1","key":"pgen.1011879.ref070","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1146\/annurev-genet-111523-102000","article-title":"M\u00fcller Glial Cell-Dependent Regeneration of the Retina in Zebrafish and Mice","volume":"58","author":"J Jui","year":"2024","journal-title":"Annu Rev Genet"},{"key":"pgen.1011879.ref071","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/0-387-32442-9_47","article-title":"Activation of cell survival signals in the goldfish retinal ganglion cells after optic nerve injury","volume":"572","author":"Y Koriyama","year":"2006","journal-title":"Adv Exp Med Biol"},{"issue":"5","key":"pgen.1011879.ref072","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1016\/j.exer.2008.07.009","article-title":"Characterization of M\u00fcller glia and neuronal progenitors during adult zebrafish retinal regeneration","volume":"87","author":"R Thummel","year":"2008","journal-title":"Exp Eye Res"},{"key":"pgen.1011879.ref073","doi-asserted-by":"crossref","first-page":"617923","DOI":"10.3389\/fcell.2020.617923","article-title":"The Regenerating Adult Zebrafish Retina Recapitulates Developmental Fate Specification Programs","volume":"8","author":"M Lahne","year":"2021","journal-title":"Front Cell Dev Biol"},{"key":"pgen.1011879.ref074","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/1471-213X-6-36","article-title":"Molecular characterization of retinal stem cells and their niches in adult zebrafish","volume":"6","author":"PA Raymond","year":"2006","journal-title":"BMC Dev Biol"},{"key":"pgen.1011879.ref075","doi-asserted-by":"crossref","first-page":"7916","DOI":"10.1038\/ncomms8916","article-title":"Turning terminally differentiated skeletal muscle cells into regenerative progenitors","volume":"6","author":"H Wang","year":"2015","journal-title":"Nature Communications"},{"key":"pgen.1011879.ref076","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1038\/s41536-020-00099-8","article-title":"Dedifferentiation: inspiration for devising engineering strategies for regenerative medicine","volume":"5","author":"Y Yao","year":"2020","journal-title":"NPJ Regen Med"},{"issue":"11","key":"pgen.1011879.ref077","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1053\/euhj.2001.2963","article-title":"Dissociation of cardiomyocyte apoptosis and dedifferentiation in infarct border zones","volume":"23","author":"GD Dispersyn","year":"2002","journal-title":"Eur Heart J"},{"issue":"9","key":"pgen.1011879.ref078","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0012559","article-title":"Dedifferentiation and proliferation of mammalian cardiomyocytes","volume":"5","author":"Y Zhang","year":"2010","journal-title":"PLoS One"},{"issue":"2","key":"pgen.1011879.ref079","doi-asserted-by":"crossref","DOI":"10.1016\/j.devcel.2021.12.012","article-title":"Adaptive differentiation promotes intestinal villus recovery","volume":"57","author":"TE Ohara","year":"2022","journal-title":"Dev Cell"},{"key":"pgen.1011879.ref080","doi-asserted-by":"crossref","first-page":"115298","DOI":"10.1016\/j.celrep.2025.115298","article-title":"Cellular rejuvenation protects neurons from inflammation-mediated cell death","volume":"44","author":"SS Drake","year":"2025","journal-title":"Cell Rep"},{"issue":"7","key":"pgen.1011879.ref081","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41582-023-00815-0","article-title":"Neural cell state shifts and fate loss in ageing and age-related diseases","volume":"19","author":"L Traxler","year":"2023","journal-title":"Nat Rev Neurol"},{"issue":"7806","key":"pgen.1011879.ref082","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1038\/s41586-020-2200-5","article-title":"Injured adult neurons regress to an embryonic transcriptional growth state","volume":"581","author":"GHD Poplawski","year":"2020","journal-title":"Nature"},{"key":"pgen.1011879.ref083","doi-asserted-by":"crossref","DOI":"10.1016\/j.neuron.2020.07.026","article-title":"Transcriptional reprogramming of distinct peripheral sensory neuron subtypes after axonal injury","volume":"108","author":"W Renthal","year":"2020","journal-title":"Neuron"},{"issue":"5","key":"pgen.1011879.ref084","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1016\/j.exer.2007.08.003","article-title":"JAK\/STAT pathway mediates retinal ganglion cell survival after acute ocular hypertension but not under normal conditions","volume":"85","author":"Y Huang","year":"2007","journal-title":"Exp Eye Res"},{"key":"pgen.1011879.ref085","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1111\/j.1460-9568.2007.05718.x","article-title":"PI3K\/akt, JAK\/STAT and MEK\/ERK pathway inhibition protects retinal ganglion cells via different mechanisms after optic nerve injury: Mechanism of pathway inhibition-induced survival","volume":"26","author":"JM Luo","year":"2007","journal-title":"Eur J Neurosci"},{"issue":"9","key":"pgen.1011879.ref086","doi-asserted-by":"crossref","DOI":"10.1038\/cddis.2013.310","article-title":"Neuronal STAT3 activation is essential for CNTF- and inflammatory stimulation-induced CNS axon regeneration","volume":"4","author":"M Leibinger","year":"2013","journal-title":"Cell Death Dis"},{"issue":"48","key":"pgen.1011879.ref087","doi-asserted-by":"crossref","first-page":"10806","DOI":"10.1523\/JNEUROSCI.3532-04.2004","article-title":"Cellular mechanisms associated with spontaneous and ciliary neurotrophic factor-cAMP-induced survival and axonal regeneration of adult retinal ganglion cells","volume":"24","author":"K Park","year":"2004","journal-title":"J Neurosci"},{"issue":"12","key":"pgen.1011879.ref088","doi-asserted-by":"crossref","first-page":"5206","DOI":"10.1167\/iovs.03-0534","article-title":"Interleukin-10 receptor signaling through STAT-3 regulates the apoptosis of retinal ganglion cells in response to stress","volume":"44","author":"ZS Boyd","year":"2003","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"4","key":"pgen.1011879.ref089","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1016\/j.neuron.2015.03.060","article-title":"Injury-induced decline of intrinsic regenerative ability revealed by quantitative proteomics","volume":"86","author":"S Belin","year":"2015","journal-title":"Neuron"},{"issue":"2","key":"pgen.1011879.ref090","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1083\/jcb.201802113","article-title":"Dual regulation of lin28a by Myc is necessary during zebrafish retina regeneration","volume":"218","author":"S Mitra","year":"2019","journal-title":"J Cell Biol"},{"key":"pgen.1011879.ref091","doi-asserted-by":"crossref","first-page":"2607","DOI":"10.1016\/j.neuron.2022.06.003","article-title":"Core transcription programs controlling injury-induced neurodegeneration of retinal ganglion cells","volume":"110","author":"F Tian","year":"2022","journal-title":"Neuron"},{"key":"pgen.1011879.ref092","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1167\/iovs.61.2.31","article-title":"Activating Transcription Factor 3 (ATF3) Protects Retinal Ganglion Cells and Promotes Functional Preservation After Optic Nerve Crush","volume":"61","author":"C Kole","year":"2020","journal-title":"Investigative Ophthalmology & Visual Science"},{"issue":"3","key":"pgen.1011879.ref093","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1016\/j.bbrc.2017.05.079","article-title":"Activating transcription factor 3 promotes spinal cord regeneration of adult zebrafish","volume":"488","author":"L-F Wang","year":"2017","journal-title":"Biochem Biophys Res Commun"},{"issue":"1","key":"pgen.1011879.ref094","doi-asserted-by":"crossref","first-page":"4418","DOI":"10.1038\/s41467-022-31960-7","article-title":"Transcription factor network analysis identifies REST\/NRSF as an intrinsic regulator of CNS regeneration in mice","volume":"13","author":"Y Cheng","year":"2022","journal-title":"Nat Commun"},{"issue":"4","key":"pgen.1011879.ref095","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1073\/pnas.1314826111","article-title":"ATF3 expression improves motor function in the ALS mouse model by promoting motor neuron survival and retaining muscle innervation","volume":"111","author":"R Seijffers","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pgen.1011879.ref096","doi-asserted-by":"crossref","first-page":"824036","DOI":"10.3389\/fcell.2022.824036","article-title":"Activating Transcription Factor 3 (ATF3) is a Highly Conserved Pro-regenerative Transcription Factor in the Vertebrate Nervous System","volume":"10","author":"HR Katz","year":"2022","journal-title":"Front Cell Dev Biol"},{"issue":"2","key":"pgen.1011879.ref097","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1016\/j.celrep.2016.03.029","article-title":"Enhanced Transcriptional Activity and Mitochondrial Localization of STAT3 Co-induce Axon Regrowth in the Adult Central Nervous System","volume":"15","author":"X Luo","year":"2016","journal-title":"Cell Rep"},{"issue":"2","key":"pgen.1011879.ref098","doi-asserted-by":"crossref","DOI":"10.1016\/j.neuron.2022.10.028","article-title":"Driving axon regeneration by orchestrating neuronal and non-neuronal innate immune responses via the IFN\u03b3-cGAS-STING axis","volume":"111","author":"X Wang","year":"2023","journal-title":"Neuron"},{"key":"pgen.1011879.ref099","doi-asserted-by":"crossref","first-page":"8477","DOI":"10.1038\/s41467-023-44142-w","article-title":"Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina","volume":"14","author":"P Lyu","year":"2023","journal-title":"Nat Commun"},{"issue":"2","key":"pgen.1011879.ref100","doi-asserted-by":"crossref","first-page":"483","DOI":"10.2337\/db16-0051","article-title":"CD40 in Retinal M\u00fcller Cells Induces P2X7-Dependent Cytokine Expression in Macrophages\/Microglia in Diabetic Mice and Development of Early Experimental Diabetic Retinopathy","volume":"66","author":"J-AC Portillo","year":"2017","journal-title":"Diabetes"},{"key":"pgen.1011879.ref101","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1016\/j.nbd.2014.09.019","article-title":"Injured adult retinal axons with Pten and Socs3 co-deletion reform active synapses with suprachiasmatic neurons","volume":"73","author":"S Li","year":"2015","journal-title":"Neurobiol Dis"},{"key":"pgen.1011879.ref102","doi-asserted-by":"crossref","first-page":"2633","DOI":"10.1038\/ncomms3633","article-title":"Cross-talk between KLF4 and STAT3 regulates axon regeneration","volume":"4","author":"S Qin","year":"2013","journal-title":"Nat Commun"},{"issue":"6","key":"pgen.1011879.ref103","article-title":"Single-cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish","volume":"37","author":"C-B Hu","year":"2023","journal-title":"FASEB J"},{"issue":"11","key":"pgen.1011879.ref104","doi-asserted-by":"crossref","first-page":"6988","DOI":"10.1074\/jbc.M707514200","article-title":"Neuronal injury-inducible gene is synergistically regulated by ATF3, c-Jun, and STAT3 through the interaction with Sp1 in damaged neurons","volume":"283","author":"S Kiryu-Seo","year":"2008","journal-title":"J Biol Chem"},{"issue":"16","key":"pgen.1011879.ref105","article-title":"Single-cell transcriptome analysis of regenerating RGCs reveals potent glaucoma neural repair genes","volume":"110","author":"L Li","year":"2022","journal-title":"Neuron"},{"issue":"7836","key":"pgen.1011879.ref106","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/s41586-020-2975-4","article-title":"Reprogramming to recover youthful epigenetic information and restore vision","volume":"588","author":"Y Lu","year":"2020","journal-title":"Nature"},{"issue":"3","key":"pgen.1011879.ref107","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1523\/JNEUROSCI.5603-11.2012","article-title":"Injury-dependent M\u00fcller glia and ganglion cell reprogramming during tissue regeneration requires Apobec2a and Apobec2b","volume":"32","author":"C Powell","year":"2012","journal-title":"J Neurosci"},{"key":"pgen.1011879.ref108","doi-asserted-by":"crossref","first-page":"3388","DOI":"10.1167\/iovs.02-0646","article-title":"A model to study differences between primary and secondary degeneration of retinal ganglion cells in rats by partial optic nerve transection","volume":"44","author":"H Levkovitch-Verbin","year":"2003","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"3","key":"pgen.1011879.ref109","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.mcn.2005.08.009","article-title":"cAMP regulates axon outgrowth and guidance during optic nerve regeneration in goldfish","volume":"30","author":"J Rodger","year":"2005","journal-title":"Mol Cell Neurosci"},{"issue":"1","key":"pgen.1011879.ref110","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1002\/cne.21477","article-title":"Regenerating optic axons restore topography after incomplete optic nerve injury","volume":"505","author":"SA Dunlop","year":"2007","journal-title":"J Comp Neurol"},{"issue":"6","key":"pgen.1011879.ref111","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1016\/S1084952102001039","article-title":"Making the connection: retinal axon guidance in the zebrafish","volume":"13","author":"J Culverwell","year":"2002","journal-title":"Semin Cell Dev Biol"},{"issue":"12","key":"pgen.1011879.ref112","doi-asserted-by":"crossref","first-page":"4513","DOI":"10.1523\/JNEUROSCI.08-12-04513.1988","article-title":"Retinotopic organization of the developing retinotectal projection in the zebrafish embryo","volume":"8","author":"CA Stuermer","year":"1988","journal-title":"J Neurosci"},{"issue":"11","key":"pgen.1011879.ref113","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.4103\/1673-5374.310670","article-title":"Mechanisms implicated in the contralateral effect in the central nervous system after unilateral injury: focus on the visual system","volume":"16","author":"F Lucas-Ruiz","year":"2021","journal-title":"Neural Regen Res"},{"issue":"22","key":"pgen.1011879.ref114","doi-asserted-by":"crossref","first-page":"5733","DOI":"10.3390\/ijms20225733","article-title":"Neuronal Death in the Contralateral Un-Injured Retina after Unilateral Axotomy: Role of Microglial Cells","volume":"20","author":"F Lucas-Ruiz","year":"2019","journal-title":"Int J Mol Sci"},{"key":"pgen.1011879.ref115","article-title":"Optic nerve crush does not induce retinal ganglion cell loss in the contralateral eye","author":"FE Schoot Uiterkamp","year":"2024","journal-title":"Neuroscience"},{"key":"pgen.1011879.ref116","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1167\/tvst.10.1.22","article-title":"When is a control not a control? Reactive microglia occur throughout the control contralateral pathway of retinal ganglion cell projections in experimental glaucoma","volume":"10","author":"JR Tribble","year":"2021","journal-title":"Transl Vis Sci Technol"},{"issue":"1","key":"pgen.1011879.ref117","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1002\/(SICI)1097-4695(199901)38:1<116::AID-NEU9>3.0.CO;2-F","article-title":"Unilateral injury to the adult rat optic nerve causes multiple cellular responses in the contralateral site","volume":"38","author":"N Bodeutsch","year":"1999","journal-title":"J Neurobiol"},{"key":"pgen.1011879.ref118","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.neuroscience.2015.09.067","article-title":"Bilateral retinal microglial response to unilateral optic nerve transection in rats","volume":"311","author":"LP Cen","year":"2015","journal-title":"Neuroscience"},{"key":"pgen.1011879.ref119","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.3389\/fnins.2019.01096","article-title":"Systemic and Intravitreal Antagonism of the TNFR1 Signaling Pathway Delays Axotomy-Induced Retinal Ganglion Cell Loss","volume":"13","author":"F Lucas-Ruiz","year":"2019","journal-title":"Front Neurosci"},{"issue":"21","key":"pgen.1011879.ref120","doi-asserted-by":"crossref","first-page":"15641","DOI":"10.3390\/ijms242115641","article-title":"Contralateral Astrocyte Response to Acute Optic Nerve Damage Is Mitigated by PANX1 Channel Activity","volume":"24","author":"JA Wurl","year":"2023","journal-title":"Int J Mol Sci"},{"issue":"31","key":"pgen.1011879.ref121","doi-asserted-by":"crossref","first-page":"18810","DOI":"10.1073\/pnas.2009425117","article-title":"Redistribution of metabolic resources through astrocyte networks mitigates neurodegenerative stress","volume":"117","author":"ML Cooper","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"17","key":"pgen.1011879.ref122","doi-asserted-by":"crossref","first-page":"2865","DOI":"10.1242\/dev.025049","article-title":"Pathfinding in a large vertebrate axon tract: isotypic interactions guide retinotectal axons at multiple choice points","volume":"135","author":"AJ Pittman","year":"2008","journal-title":"Development"},{"issue":"2","key":"pgen.1011879.ref123","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1016\/j.celrep.2014.10.022","article-title":"Retinal Injury, Growth Factors, and Cytokines Converge on \u03b2-Catenin and pStat3 Signaling to Stimulate Retina Regeneration","volume":"9","author":"J Wan","year":"2014","journal-title":"Cell Reports"},{"key":"pgen.1011879.ref124","unstructured":"Cell Ranger Pipeline version 6.1.2. In: https:\/\/www.10xgenomics.com\/ [Internet]. Available: https:\/\/www.10xgenomics.com\/support\/software\/cell-ranger\/latest\/tutorials\/cr-tutorial-ct"},{"issue":"2","key":"pgen.1011879.ref125","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Y Hao","year":"2024","journal-title":"Nat Biotechnol"},{"key":"pgen.1011879.ref126","doi-asserted-by":"crossref","first-page":"979","DOI":"10.12688\/f1000research.73600.1","article-title":"Doublet identification in single-cell sequencing data using scDblFinder","volume":"10","author":"P-L Germain","year":"2021","journal-title":"F1000Res"},{"key":"pgen.1011879.ref127","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-98141-3","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"H Wickham","year":"2009"},{"key":"pgen.1011879.ref128","first-page":"2122","article-title":"A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor","volume":"5","author":"ATL Lun","year":"2016","journal-title":"F1000Res"},{"issue":"2","key":"pgen.1011879.ref129","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/s41592-019-0654-x","article-title":"Orchestrating single-cell analysis with Bioconductor","volume":"17","author":"RA Amezquita","year":"2020","journal-title":"Nat Methods"},{"issue":"1","key":"pgen.1011879.ref130","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"MD Robinson","year":"2010","journal-title":"Bioinformatics"},{"issue":"8","key":"pgen.1011879.ref131","doi-asserted-by":"crossref","first-page":"2628","DOI":"10.1093\/bioinformatics\/btz931","article-title":"ShinyGO: a graphical gene-set enrichment tool for animals and plants","volume":"36","author":"SX Ge","year":"2020","journal-title":"Bioinformatics"},{"issue":"8","key":"pgen.1011879.ref132","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/nprot.2009.97","article-title":"Mapping identifiers for the integration of genomic datasets with the R\/Bioconductor package biomaRt","volume":"4","author":"S Durinck","year":"2009","journal-title":"Nat Protoc"},{"issue":"16","key":"pgen.1011879.ref133","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1093\/bioinformatics\/bti525","article-title":"BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis","volume":"21","author":"S Durinck","year":"2005","journal-title":"Bioinformatics"},{"issue":"21","key":"pgen.1011879.ref134","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2017198118","article-title":"The immune response is a critical regulator of zebrafish retinal pigment epithelium regeneration","volume":"118","author":"LL Leach","year":"2021","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"pgen.1011879.ref135","article-title":"Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust","volume":"145","author":"HMT Choi","year":"2018","journal-title":"Development"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1011879","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T00:00:00Z","timestamp":1758672000000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1011879","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T17:52:15Z","timestamp":1758736335000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1011879"}},"subtitle":[],"editor":[{"given":"Brian D.","family":"Perkins,","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,9,19]]},"references-count":135,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2025,9,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1011879","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pgen.1011879","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,19]]}}}