{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE311nnn/GSE311199/"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Mus musculus"," Homo sapiens"],"gds_type":[" Genome binding/occupancy profiling by high throughput sequencing"," Other","Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE311199"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Integrative spatial profiling of 3D genome organization and gene expression in complex tissue","description":"Three-dimensional genome organization shapes transcriptional regulation, yet measuring its spatial coordination in situ within intact tissues remains challenging. We present Spatial Hi-C-RNA, a multimodal platform that simultaneously maps genome-wide chromatin contacts and transcriptomes from the same tissue section at near single-cell resolution. Across mouse brain, developing embryos, and human melanoma, Spatial Hi-C-RNA generated multimodal maps that aligned with tissue anatomy while revealing complementary chromatin- and RNA-defined spatial patterns. Multiscale features, including A/B compartments, topologically associating domains, and chromatin loops, were associated with region- and cell-type-specific transcriptional programs. In mouse embryos, Spatial Hi-C-RNA resolved coordinated chromatin and transcriptional remodeling during neuronal maturation across developmental stages. In human melanoma, chromatin architecture delineated intratumoral subregions not detected by RNA alone and linked tumor-state transitions to changes in compartments, domain boundaries, and regulatory programs. Spatial Hi-C-RNA thus provides a broadly applicable framework for investigating genome structure–function relationships in development and disease within native tissue environments.","dates":{"publication":"2026/07/24"},"accession":"GSE311199","cross_references":{"GSM":["GSM9738333","GSM9738332","GSM9320919","GSM9738331","GSM9738330","GSM9320924","GSM9320922","GSM9320923","GSM9320917","GSM9320918","GSM9320916","GSM9320920","GSM9320921","GSM9738329","GSM9738334"],"GPL":["34284","34290"],"GSE":["311199"],"taxon":["Mus musculus"," Homo sapiens"],"PMID":["[42641604]"]}}