Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

C42B Micro-C

ABSTRACT: We performed Hi-C, Micro-C, and capture Micro-C in human prostate cancer cells and compared chromatin interactions called using different methods. By integrating Micro-C with NOMe-seq, ChIP-seq, and RNA-seq, we investigated the relationships among nucleosome positioning of regulatory elements, chromatin interactions, and transcription. This work provides a framework for understanding the chromatin interactions among regulatory elements, nucleosome-depleted regions, and transcription.

ORGANISM(S): Homo sapiens

PROVIDER: GSE204997 | GEO | 2023/01/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

C42B Capture Micro-C

Project description:We performed Hi-C, Micro-C, and capture Micro-C in human prostate cancer cells and compared chromatin interactions called using different methods. By integrating Micro-C with NOMe-seq, ChIP-seq, and RNA-seq, we investigated the relationships among nucleosome positioning of regulatory elements, chromatin interactions, and transcription. This work provides a framework for understanding the chromatin interactions among regulatory elements, nucleosome-depleted regions, and transcription.

2023-01-11 | GSE204995 | GEO

C42B HiC

2023-01-11 | GSE204996 | GEO

C42B RNA-seq

2023-01-11 | GSE204999 | GEO

C42B NOMe-seq

2023-01-11 | GSE204998 | GEO

Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C

Project description:Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C

| PRJNA843042 | ENA

C42B Micro-C

Project description:C42B Micro-C

| PRJNA843049 | ENA

Nucleosome Occupancy and Methylome Sequencing (NOMe-seq) analysis using SureSelectXT Methyl-Seq Target Enrichment System

Project description:Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Nucleosome occupancy and methylome sequencing (NOMe-seq) has been developed for simultaneously profiling of chromatin accessibility and DNA methylation on single molecules. In this study, we combined the principle of NOMe-seq with targeted bisulfite sequencing method to analyze the genome-wide nucleosome occupancy and chromatin accessibility in the promoter and enhancer regions of over 20,000 genes. In addition, we developed CAME, a seed-extension based approach that identifies chromatin accessibility from NOMe-seq. Our results show that our method not only can precisely identify chromatin accessibility but also outperforms other methods.

2016-09-13 | GSE86823 | GEO

C42B NOMe-seq

Project description:C42B NOMe-seq

| PRJNA843048 | ENA

C42B Capture Micro-C

Project description:C42B Capture Micro-C

| PRJNA843051 | ENA

NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

Project description:Cis-regulatory elements coordinate the regulation of their targeted genes’ expression. However, the joint measurement of cis-regulatory elements’ activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.

2023-02-28 | GSE189158 | GEO

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