{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T22:01:37Z","timestamp":1791928897002,"version":"4.3.4"},"reference-count":49,"publisher":"Association for Research in Vision and Ophthalmology (ARVO)","issue":"13","license":[{"start":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T00:00:00Z","timestamp":1759881600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Invest. Ophthalmol. Vis. Sci."],"published-print":{"date-parts":[[2025,10,8]]},"DOI":"10.1167\/iovs.66.13.11","type":"journal-article","created":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T13:30:42Z","timestamp":1759930242000},"page":"11","source":"Crossref","is-referenced-by-count":1,"title":["Comparative Transcriptomic Profiling of Corneal Compartments Using Single-Cell and Single-Nucleus Sequencing"],"prefix":"10.1167","volume":"66","author":[{"given":"Hongran","family":"Zhao","sequence":"first","affiliation":[{"name":"Eye Institute of Shandong First Medical University, Qingdao, People's Republic of China"},{"name":"State Key Laboratory Cultivation Base, Shandong Key Laboratory of Eye Diseases, Qingdao, People's Republic of China"},{"name":"School of Ophthalmology, Shandong First Medical University, Qingdao, People's Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyu","family":"Li","sequence":"additional","affiliation":[{"name":"Eye Institute of Shandong First Medical University, Qingdao, People's Republic of China"},{"name":"State Key Laboratory Cultivation Base, Shandong Key Laboratory of Eye Diseases, Qingdao, People's Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaowen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Eye Institute of Shandong First Medical University, Qingdao, People's Republic of China"},{"name":"State Key Laboratory Cultivation Base, Shandong Key Laboratory of Eye Diseases, Qingdao, People's Republic of China"},{"name":"School of Ophthalmology, Shandong First Medical University, Qingdao, People's Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingjun","family":"Zhou","sequence":"additional","affiliation":[{"name":"Eye Institute of Shandong First Medical University, Qingdao, People's Republic of China"},{"name":"State Key Laboratory Cultivation Base, Shandong Key Laboratory of Eye Diseases, Qingdao, People's Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengqian","family":"Dou","sequence":"additional","affiliation":[{"name":"Eye Institute of Shandong First Medical University, Qingdao, People's Republic of China"},{"name":"State Key Laboratory Cultivation Base, Shandong Key Laboratory of Eye Diseases, Qingdao, People's Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lixin","family":"Xie","sequence":"additional","affiliation":[{"name":"Eye Institute of Shandong First Medical University, Qingdao, People's Republic of China"},{"name":"State Key Laboratory Cultivation Base, Shandong Key Laboratory of Eye Diseases, Qingdao, People's Republic of China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"27","reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"101275","DOI":"10.1016\/j.preteyeres.2024.101275","article-title":"Cell therapy in the cornea: the emerging role of microenvironment","volume":"102","author":"Suanno","year":"2024","journal-title":"Prog Retin Eye Res"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/bs.pmbts.2015.04.001","article-title":"Overview of the cornea: structure, function, and development","volume":"134","author":"Eghrari","year":"2015","journal-title":"Prog Mol Biol Transl Sci"},{"issue":"10","key":"bib3","doi-asserted-by":"publisher","first-page":"3570","DOI":"10.1167\/iovs.19-27656","article-title":"Single-cell RNA transcriptome helps define the limbal\/corneal epithelial stem\/early transit amplifying cells and how autophagy affects this population","volume":"60","author":"Kaplan","year":"2019","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"4","key":"bib4","doi-asserted-by":"publisher","first-page":"672","DOI":"10.1016\/j.jtos.2020.07.009","article-title":"Tissue engineered corneal epithelium derived from clinical-grade human embryonic stem cells","volume":"18","author":"He","year":"2020","journal-title":"Ocul Surf"},{"issue":"16","key":"bib5","doi-asserted-by":"publisher","first-page":"3334","DOI":"10.1038\/s41433-023-02539-3","article-title":"Single-cell transcriptomics of the ocular anterior segment: a comprehensive review","volume":"37","author":"Ahsanuddin","year":"2023","journal-title":"Eye"},{"issue":"13","key":"bib6","doi-asserted-by":"publisher","first-page":"1808","DOI":"10.3390\/cells12131808","article-title":"Single-cell RNA sequencing: opportunities and challenges for studies on corneal biology in health and disease","volume":"12","author":"Arts","year":"2023","journal-title":"Cells"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"109544","DOI":"10.1016\/j.exer.2023.109544","article-title":"Optimization of method for achieving a single-cell suspension from mouse corneas","volume":"233","author":"Liu","year":"2023","journal-title":"Exp Eye Res"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"101234","DOI":"10.1016\/j.preteyeres.2023.101234","article-title":"Squishy matters \u2013 corneal mechanobiology in health and disease","volume":"99","author":"Thomasy","year":"2024","journal-title":"Prog Retin Eye Res"},{"issue":"10","key":"bib9","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1038\/nmeth.4407","article-title":"Massively parallel single-nucleus RNA-seq with DroNc-seq","volume":"14","author":"Habib","year":"2017","journal-title":"Nat Methods"},{"issue":"1","key":"bib10","doi-asserted-by":"publisher","first-page":"2907","DOI":"10.1038\/s41467-019-10756-2","article-title":"Nuclei multiplexing with barcoded antibodies for single-nucleus genomics","volume":"10","author":"Gaublomme","year":"2019","journal-title":"Nat Commun"},{"issue":"1","key":"bib11","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1681\/ASN.2018090912","article-title":"Advantages of single-nucleus over single-cell RNA sequencing of adult kidney: rare cell types and novel cell states revealed in fibrosis","volume":"30","author":"Wu","year":"2019","journal-title":"J Am Soc Nephrol"},{"issue":"6302","key":"bib12","doi-asserted-by":"publisher","first-page":"925","DOI":"10.1126\/science.aad7038","article-title":"Div-Seq: single-nucleus RNA-seq reveals dynamics of rare adult newborn neurons","volume":"353","author":"Habib","year":"2016","journal-title":"Science"},{"issue":"1","key":"bib13","doi-asserted-by":"publisher","first-page":"111628","DOI":"10.1016\/j.isci.2024.111628","article-title":"Exploring the utility of snRNA-seq in profiling human bladder tissue: a comprehensive comparison with scRNA-seq","volume":"28","author":"Santo","year":"2024","journal-title":"iScience"},{"key":"bib14","first-page":"0182","article-title":"Cold-induced reprogramming of subcutaneous white adipose tissue assessed by single-cell and single-nucleus RNA sequencing","volume":"6","author":"Liu","year":"2023","journal-title":"Research (Wash D C)"},{"issue":"4","key":"bib15","doi-asserted-by":"publisher","first-page":"100335","DOI":"10.1016\/j.xops.2023.100335","article-title":"Comparative analysis of single-cell and single-nucleus RNA-sequencing in a rabbit model of retinal detachment-related proliferative vitreoretinopathy","volume":"3","author":"Santiago","year":"2023","journal-title":"Ophthalmol Sci"},{"issue":"1","key":"bib16","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1186\/s12885-023-10977-1","article-title":"Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing","volume":"23","author":"Truong","year":"2023","journal-title":"BMC Cancer"},{"issue":"1","key":"bib17","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1038\/s42003-024-07445-2","article-title":"Optimized methods for scRNA-seq and snRNA-seq of skeletal muscle stored in nucleic acid stabilizing preservative","volume":"8","author":"Heuston","year":"2025","journal-title":"Commun Biol"},{"issue":"5","key":"bib18","doi-asserted-by":"publisher","first-page":"792","DOI":"10.1038\/s41591-020-0844-1","article-title":"A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors","volume":"26","author":"Slyper","year":"2020","journal-title":"Nat Med"},{"issue":"10","key":"bib19","doi-asserted-by":"publisher","first-page":"1633","DOI":"10.3390\/cells11101633","article-title":"Single-cell and single-nucleus RNAseq analysis of adult neurogenesis","volume":"11","author":"Kalinina","year":"2022","journal-title":"Cells"},{"issue":"12","key":"bib20","doi-asserted-by":"publisher","first-page":"2128","DOI":"10.1038\/s12276-022-00892-z","article-title":"Comparison of cell type distribution between single-cell and single-nucleus RNA sequencing: enrichment of adherent cell types in single-nucleus RNA sequencing","volume":"54","author":"Oh","year":"2022","journal-title":"Exp Mol Med"},{"issue":"1","key":"bib21","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1186\/s13073-022-01055-5","article-title":"Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival","volume":"14","author":"Alvarez","year":"2022","journal-title":"Genome Med"},{"issue":"4","key":"bib22","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1002\/hep4.1854","article-title":"Single-cell, single-nucleus, and spatial RNA sequencing of the human liver identifies cholangiocyte and mesenchymal heterogeneity","volume":"6","author":"Andrews","year":"2021","journal-title":"Hepatol Commun"},{"issue":"8","key":"bib23","doi-asserted-by":"publisher","first-page":"1838","DOI":"10.1681\/ASN.2021020157","article-title":"Current methodological challenges of single-cell and single-nucleus RNA-sequencing in glomerular diseases","volume":"32","author":"Deleersnijder","year":"2021","journal-title":"J Am Soc Nephrol"},{"issue":"1","key":"bib24","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1186\/s13059-020-02048-6","article-title":"Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows","volume":"21","author":"Denisenko","year":"2020","journal-title":"Genome Biol"},{"issue":"2","key":"bib25","doi-asserted-by":"publisher","first-page":"F171","DOI":"10.1152\/ajprenal.00453.2021","article-title":"Single cell versus single nucleus: transcriptome differences in the murine kidney after ischemia-reperfusion injury","volume":"323","author":"Gaedcke","year":"2022","journal-title":"Am J Physiol Renal Physiol"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1016\/j.omtn.2022.01.005","article-title":"Heterogeneity of human corneal endothelium implicates lncRNA NEAT1 in Fuchs endothelial corneal dystrophy","volume":"27","author":"Wang","year":"2022","journal-title":"Mol Ther Nucleic Acids"},{"issue":"7","key":"bib27","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"issue":"5","key":"bib28","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat Biotechnol"},{"issue":"29","key":"bib29","doi-asserted-by":"publisher","first-page":"e2200914119","DOI":"10.1073\/pnas.2200914119","article-title":"Cell atlas of the human ocular anterior segment: tissue-specific and shared cell types","volume":"119","author":"van Zyl","year":"2022","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1","key":"bib30","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1186\/s13287-024-03816-y","article-title":"Decoding cellular plasticity and niche regulation of limbal stem cells during corneal wound healing","volume":"15","author":"Sun","year":"2024","journal-title":"Stem Cell Res Ther"},{"issue":"7719","key":"bib31","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA velocity of single cells","volume":"560","author":"La Manno","year":"2018","journal-title":"Nature"},{"issue":"10","key":"bib32","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1038\/nmeth.4437","article-title":"Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations","volume":"14","author":"van den Brink","year":"2017","journal-title":"Nat Methods"},{"issue":"7","key":"bib33","doi-asserted-by":"publisher","first-page":"1248","DOI":"10.1016\/j.stem.2021.04.003","article-title":"Discrete limbal epithelial stem cell populations mediate corneal homeostasis and wound healing","volume":"28","author":"Altshuler","year":"2021","journal-title":"Cell Stem Cell"},{"issue":"1","key":"bib34","doi-asserted-by":"publisher","first-page":"5675","DOI":"10.1038\/s41467-021-25968-8","article-title":"Multi-species single-cell transcriptomic analysis of ocular compartment regulons","volume":"12","author":"Gautam","year":"2021","journal-title":"Nat Commun"},{"issue":"2","key":"bib35","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1167\/iovs.66.2.64","article-title":"Identification of Wnt-5a receptors important in diabetic and non-diabetic corneal epithelial wound healing","volume":"66","author":"Shah","year":"2025","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"13","key":"bib36","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1167\/iovs.64.13.5","article-title":"Single-cell transcriptomics reveals cellular heterogeneity and complex cell-cell communication networks in the mouse cornea","volume":"64","author":"Wu","year":"2023","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"9","key":"bib37","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1167\/iovs.62.9.36","article-title":"Single-cell transcriptomics identifies a unique entity and signature markers of transit-amplifying cells in human corneal limbus","volume":"62","author":"Li","year":"2021","journal-title":"Invest Ophthalmol Vis Sci"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/j.jtos.2021.04.010","article-title":"Molecular identity of human limbal heterogeneity involved in corneal homeostasis and privilege","volume":"21","author":"Dou","year":"2021","journal-title":"Ocul Surf"},{"key":"bib39","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.jtos.2020.12.004","article-title":"Single-cell transcriptomics identifies limbal stem cell population and cell types mapping its differentiation trajectory in limbal basal epithelium of human cornea","volume":"20","author":"Li","year":"2021","journal-title":"Ocul Surf"},{"issue":"1","key":"bib40","doi-asserted-by":"publisher","first-page":"16323","DOI":"10.1038\/s41598-021-94933-8","article-title":"Molecular characteristics and spatial distribution of adult human corneal cell subtypes","volume":"11","author":"Ligocki","year":"2021","journal-title":"Sci Rep"},{"issue":"3","key":"bib41","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1167\/iovs.66.3.9","article-title":"Single-cell multiomics analysis of early wound response programs in the mouse corneal epithelium","volume":"66","author":"Lu","year":"2025","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"3","key":"bib42","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1167\/iovs.64.3.30","article-title":"Integrative single-cell RNA-Seq and ATAC-Seq analysis of mouse corneal epithelial cells","volume":"64","author":"Lu","year":"2023","journal-title":"Invest Ophthalmol Vis Sci"},{"issue":"1","key":"bib43","doi-asserted-by":"publisher","first-page":"21727","DOI":"10.1038\/s41598-021-01015-w","article-title":"Single cell transcriptomics reveals the heterogeneity of the human cornea to identify novel markers of the limbus and stroma","volume":"11","author":"Catal\u00e0","year":"2021","journal-title":"Sci Rep"},{"issue":"6","key":"bib44","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/s41587-020-0465-8","article-title":"Systematic comparison of single-cell and single-nucleus RNA-sequencing methods","volume":"38","author":"Ding","year":"2020","journal-title":"Nat Biotechnol"},{"key":"bib45","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/j.jtos.2025.02.010","article-title":"Decoding the corneal immune microenvironment in healthy and diabetic mice during corneal wound healing","volume":"37","author":"Lin","year":"2025","journal-title":"Ocul Surf"},{"issue":"12","key":"bib46","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1167\/iovs.65.12.29","article-title":"Mouse corneal immune cell heterogeneity revealed by single-cell RNA sequencing","volume":"65","author":"Yaman","year":"2024","journal-title":"Invest Ophthalmol Vis Sci"},{"key":"bib47","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1016\/j.jtos.2021.03.010","article-title":"A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells","volume":"21","author":"Collin","year":"2021","journal-title":"Ocul Surf"},{"issue":"1","key":"bib48","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1038\/s41421-022-00397-z","article-title":"Single-cell atlas of keratoconus corneas revealed aberrant transcriptional signatures and implicated mechanical stretch as a trigger for keratoconus pathogenesis","volume":"8","author":"Dou","year":"2022","journal-title":"Cell Discov"},{"key":"bib49","doi-asserted-by":"publisher","first-page":"113811","DOI":"10.1016\/j.jconrel.2025.113811","article-title":"Delivery of Itgb1-siRNA by triptolide-modified and anti-Flt1 peptide-guided ionizable cationic LNPs for targeted therapy of corneal neovascularization","volume":"383","author":"Song","year":"2025","journal-title":"J Control Release"}],"container-title":["Investigative Ophthalmology & Visual Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/iovs.arvojournals.org\/article.aspx?articleid=2810939","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T21:31:57Z","timestamp":1791927117000},"score":1,"resource":{"primary":{"URL":"https:\/\/iovs.arvojournals.org\/article.aspx?articleid=2810939"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,8]]},"references-count":49,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2025,10,1]]}},"URL":"https:\/\/doi.org\/10.1167\/iovs.66.13.11","relation":{},"ISSN":["1552-5783"],"issn-type":[{"value":"1552-5783","type":"print"}],"subject":[],"published":{"date-parts":[[2025,10,8]]}}}