Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues

ABSTRACT: scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues

PROVIDER: PRJNA1308126 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_brain_scHiCAR_1]

Project 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.

2025-08-30 | GSE305439 | GEO

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_brain_scHiCAR_2]

2025-08-30 | GSE267126 | GEO

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [cellline_scHiCAR]

2025-08-30 | GSE267117 | GEO

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_skeletal_muscle_scHiCAR]

2025-08-30 | GSE304674 | GEO

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissue [mouse_brain_bulk_HiCAR]

2025-08-30 | GSE267118 | GEO

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_brain_scHiCAR_2]

Project description:scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_brain_scHiCAR_2]

| PRJNA1109822 | ENA

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_brain_scHiCAR_1]

Project description:scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_brain_scHiCAR_1]

| PRJNA1305748 | ENA

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [cellline_scHiCAR]

Project description:scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [cellline_scHiCAR]

| PRJNA1109789 | ENA

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_skeletal_muscle_scHiCAR]

Project description:scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissues [mouse_skeletal_muscle_scHiCAR]

| PRJNA1302313 | ENA

scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissue [mouse_brain_bulk_HiCAR]

Project description:scHiCAR: a tri-modal single-cell genomics technology for integrated transcriptome, epigenome, and 3D genome analysis in complex tissue [mouse_brain_bulk_HiCAR]

| PRJNA1109788 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data