{"database":"ENA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["Diao Lab, Cell Biology, Duke University"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA1109822"],"scientific_name":["Mus musculus"],"long_description":["The three-dimensional (3D) organization of cis-regulatory elements (CREs) plays a central role in transcription control. However, capturing transcriptome, epigenome, and 3D genome from the same single cells remains technically challenging. Here, we present scHiCAR (single-cell Hi-C with ATAC and RNA-seq), a combinatorial barcoding-based method that simultaneously profiles mRNA, open chromatin, and chromosome-conformation-capture from the same cells. Compared to existing single-cell 3D genome methods, scHiCAR more efficiently enriches long-range cis-interactions anchored at candidate CREs (cCREs). Applied to 1.62 million mouse brain cells and complemented with a deep learning-based loop caller, scHiCAR accurately defines cell-type-specific transcriptomes, accessible cCREs, and 5kb-resolution enhancer-promoter pairs across 22 brain cell types. scHiCAR also performs robustly in challenging tissues such as skeletal muscle, enabling tri-modal single-cell level analysis of gene regulation dynamics during muscle stem cell regeneration. scHiCAR offers a scalable, efficient, and cost-effective platform for studying gene regulatory landscapes in complex tissues at single-cell resolution. Overall design: To demonstrate the utility of scHiCAR for high-throughput analysis, we profiled 1.62 million mouse brain nuclei with matched RNA and DNA barcodes from four batches experiments, with three pilot experiments and one large scale experiment recovering 1.2M nuclei."],"repository":["ENA"],"additional_accession":[]},"is_claimable":false,"name":"scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_brain_scHiCAR_2]","description":"scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_brain_scHiCAR_2]","dates":{"last_updated":"2025-09-24","first_public":"2025-09-08"},"accession":"PRJNA1109822","cross_references":{"GEO":["GSE267126"],"taxon":["10090"]}}