{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE307nnn/GSE307363/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"species":["Homo sapiens"],"gds_type":["Genome binding/occupancy profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE307363"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"3D epigenomic landscape of human retinal pigment epithelium [CUT&Tag]","description":"Retinal pigment epithelium (RPE) serves as a vital guardian of visual function, with its dysfunction driving pathogenesis in various retinal diseases, including age-related macular degeneration and inherited retinal disorders. While ongoing RPE cells transplantation clinical trials worldwide, the absence of standardized quality metrics for stem cell-derived RPE represents a significant gap. In this study, we aim to systematically dissect epigenomic divergence among human primary RPE (hRPE), induced pluripotent stem cell-derived RPE (iPSC-RPE), and immortalized ARPE-19 cells through multi-omic analyses. Our study elucidated the distinct functional characteristics of the three types of RPE and their underlying epigenetic regulatory mechanisms, with a particular focus on the development and functional maturation of iPSC-RPE. We further revealed cell-type-specific regulatory blueprints: hRPE exhibits strong extracellular matrix (ECM) organization capacity through 3D-epigenomic (3D genome folding and epigenomic state) regulation, as exemplified by the enrichment of the RUNX1 motif, whereas iPSC-RPE retains signatures of RPE development and weak ECM function, marked by transcription factors such as Hand1, OTX2, PAX6, and ECM-associated genes. On the other hand, ARPE-19 exhibits greater cell proliferation ability and specifically regulated by transcription factors such as KLF5. Together, our data greatly advance our understanding of RPE biology and provide a robust foundation for optimizing iPSC-RPE differentiation protocols and developing innovative therapeutic strategies for retinal diseases.","dates":{"publication":"2026/07/26"},"accession":"GSE307363","cross_references":{"GSM":["GSM9222844","GSM9883418","GSM9222822","GSM9883419","GSM9222823","GSM9222842","GSM9222820","GSM9222821","GSM9222843","GSM9222840","GSM9222841","GSM9222819","GSM9222839","GSM9222817","GSM9222818","GSM9222815","GSM9222837","GSM9222838","GSM9222816","GSM9222835","GSM9222813","GSM9222836","GSM9222814","GSM9222833","GSM9222834","GSM9222831","GSM9222832","GSM9222830","GSM9883412","GSM9222828","GSM9883413","GSM9222829","GSM9883414","GSM9222826","GSM9883415","GSM9222827","GSM9222824","GSM9883416","GSM9222825","GSM9883417"],"GPL":["24676"],"GSE":["307363"],"taxon":["Homo sapiens"]}}