Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Droplet Hi-C enables scalable, single-cell profiling of chromatin architecture in heterogeneous tissues

ABSTRACT: Current methods for analyzing chromatin architecture are not readily scalable to heterogeneous tissues. Here we introduce Droplet Hi-C, which uses a commercial microfluidic device for high-throughput, single-cell chromatin conformation profiling in droplets. Using Droplet Hi-C, we mapped the chromatin architecture of the mouse cortex and analyzed gene regulatory programs in major cortical cell types. In addition, we used this technique to detect copy number variations, structural variations and extrachromosomal DNA in human glioblastoma, colorectal and blood cancer cells, revealing clonal dynamics and other oncogenic events during treatment. We refined the technique to allow joint profiling of chromatin architecture and transcriptome in single cells, facilitating exploration of the links between chromatin architecture and gene expression in both normal tissues and tumors. Thus, Droplet Hi-C both addresses critical gaps in chromatin analysis of heterogeneous tissues and enhances understanding of gene regulation.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE253407 | GEO | 2024/09/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Droplet barcoding for single cell transcriptomics applied to embryonic stem cells

Project description:Recently, RNA sequencing has achieved single cell resolution, but what is limiting is an effective way to routinely isolate and process large numbers of individual cells for in-depth sequencing, and to do so quantitatively. We have developed a droplet-microfluidic approach for parallel barcoding thousands of individual cells for subsequent RNA profiling by next-generation sequencing. This high-throughput method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. Using this technique, we analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after LIF withdrawal. The reproducibility and low noise of this high-throughput single cell data allowed us to deconstruct cell populations and infer gene expression relationships. A total of 8 single cell data sets are submitted: 3 for mouse embryonic stem (ES) cells (1 biological replicate, 2 technical replicates); 3 samples following LIF withdrawal (days 2,4, 7); one pure RNA data set (from human lymphoblast K562 cells); and one sample of single K562 cells.

2015-05-20 | E-GEOD-65525 | biostudies-arrayexpress

Droplet barcoding for single cell transcriptomics applied to embryonic stem cells

2015-05-20 | GSE65525 | GEO

A cookbook of DNase Hi-C

Project description:Hi-C technique is widely used to study 3-dimensional chromatin architecture and assemble genomes. Conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in non-uniform genomic coverage. Using sequence-agnostic restriction enzymes such as DNAse I could overcome this limitation. Here we compared different DNAse Hi-C protocols and identified several critical steps which significantly impact protocol efficiency. We proposed a new robust protocol for preparation of DNAse Hi-C libraries, supplemented with experimental controls and computational pipeline for evaluation of libraries quality and data analysis.

2020-10-31 | GSE160484 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Blood]

Project description:While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. This approach enables robust cell-typing of complex tissues and reveals a de novo atlas of cellular and epigenomic diversity across many cell types and cell stages.

2019-05-02 | GSE123578 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Validation]

2019-06-20 | GSE133071 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [GM12878]

2019-05-02 | GSE130537 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [PBMC]

2019-05-02 | GSE123577 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Bone marrow]

2019-05-02 | GSE123580 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [species mixture]

2019-05-02 | GSE123579 | GEO

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [mouse brain]