Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

ABSTRACT: Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

PROVIDER: PRJNA541105 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9010630_1.fastq.gz	Fastqsanger.gz
	SRR9010630_2.fastq.gz	Fastqsanger.gz
	SRR9010640_1.fastq.gz	Fastqsanger.gz
	SRR9010640_2.fastq.gz	Fastqsanger.gz
	SRR9010650_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8476

Similar Datasets

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

Project description:Dynamic 3D chromatin conformation is a critical mechanism for gene regulation during development and disease. Despite this, profiling of 3D genome structure from complex tissues with cell-type specific resolution remains challenging. Recent efforts have demonstrated that cell-type specific epigenomic features can be resolved in complex tissues using single-cell assays. However, it remains unclear whether single-cell Chromatin Conformation Capture (3C) or Hi-C profiles can effectively identify cell types and reconstruct cell-type specific chromatin conformation maps. To address these challenges, we have developed single-nucleus methyl-3C sequencing (sn-m3C-seq) to capture chromatin organization and DNA methylation information and robustly separate heterogeneous cell types. Applying this method to >4,200 single human brain prefrontal cortex cells, we reconstruct cell-type specific chromatin conformation maps from 14 cortical cell types. These datasets reveal the genome-wide association between cell-type specific chromatin conformation and differential DNA methylation, suggesting pervasive interactions between epigenetic processes regulating gene expression.

2019-09-09 | GSE130711 | GEO

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.

Project description:Dynamic three-dimensional chromatin conformation is a critical mechanism for gene regulation during development and disease. Despite this, profiling of three-dimensional genome structure from complex tissues with cell-type specific resolution remains challenging. Recent efforts have demonstrated that cell-type specific epigenomic features can be resolved in complex tissues using single-cell assays. However, it remains unclear whether single-cell chromatin conformation capture (3C) or Hi-C profiles can effectively identify cell types and reconstruct cell-type specific chromatin conformation maps. To address these challenges, we have developed single-nucleus methyl-3C sequencing to capture chromatin organization and DNA methylation information and robustly separate heterogeneous cell types. Applying this method to >4,200 single human brain prefrontal cortex cells, we reconstruct cell-type specific chromatin conformation maps from 14 cortical cell types. These datasets reveal the genome-wide association between cell-type specific chromatin conformation and differential DNA methylation, suggesting pervasive interactions between epigenetic processes regulating gene expression.

| S-EPMC6765423 | biostudies-literature

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics

Project description:Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics

| PRJNA1206133 | ENA

Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription

Project description:Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription

| PRJNA869722 | ENA

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (cell-line)

Project description:Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (cell-line)

| PRJNA1202075 | ENA

3D chromatin structure in colon cancer

Project description:We report the application of in situ Hi-C technology to 40 colorectal cancer patients and 10 paired-normal tissue to identify CRC specific changes in 3D chromatin structure. The chromatin contact matrices were generated by the sequencing data and image processing/deep learning-based algorithm was proposed to identify long-range abnormal chromatin interaction patterns in the contact matrices. The tumor specific 3D chromatin structure changes and the enhancer-promoter rewiring mediated by the identified chromatin structure changes were analyzed. The complex chromosome-wide rearrangements such as chromothripsis and its effect to 3D chromatin structure were also observed.

2023-07-27 | GSE137188 | GEO

3D chromatin structure in colon cancer

Project description:3D chromatin structure in colon cancer

| PRJNA564773 | ENA

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (dscHi-C multiome)

Project description:Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (dscHi-C multiome)

| PRJNA1202085 | ENA

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (b12-mouse-brain)

Project description:Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (b12-mouse-brain)

| PRJNA1202080 | ENA

Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (b3-mouse-brain)

Project description:Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (b3-mouse-brain)

| PRJNA1206136 | ENA