Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

C42B RNA-seq

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: GSE204999 | 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 HiC

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 | GSE204996 | GEO

C42B NOMe-seq

2023-01-11 | GSE204998 | GEO

C42B Micro-C

2023-01-11 | GSE204997 | GEO

C42B Capture Micro-C

2023-01-11 | GSE204995 | GEO

Genome-wide mapping of nucleosome positioning and DNA methylation within Individual DNA molecules

Project description:DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring significant amounts of material and varying enzyme concentrations. We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. Using a novel bioinformatics pipeline we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions, that is not present at promoters. We further show that the extent of nucleosome depletion at promoters is directly correlated to expression level and can accommodate multiple nucleosomes and provide genome-wide evidence that expressed non-CpG island promoters are nucleosome depleted. Importantly, NOMe-seq obtains DNA methylation and nucleosome positioning information from the same DNA molecule, giving the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule and thus, single cell level that can be used to monitor disease progression and response to therapy. Nucleosome Occupancy and Methylome-Sequencing (NOMe-Seq) on IMR90 cell line and 2 GBM cell lines

2012-09-12 | E-GEOD-40770 | biostudies-arrayexpress

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

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

Project description:Gaining insights into the regulatory mechanisms that underlie the pervasive transcriptional variation observed between individual cells necessitates the development of methods that measure chromatin organization in single cells. Nucleosome Occupancy and Methylome-sequencing (NOMe-seq) employs a GpC methyltransferase to detect accessible chromatin and has been used to map nucleosome positioning and DNA methylation genome-wide in bulk samples. Here I provide proof-of-principle that NOMe-seq can be adapted to measure chromatin accessibility and endogenous DNA methylation in single cells (scNOMe-seq). scNOMe-seq recovered characteristic accessibility and DNA methylation patterns at DNase Hypersensitive sites and enabled direct estimation of the number of accessible DHS sites within an individual cell. In addition, scNOMe-seq provided high resolution of chromatin accessibility within individual loci which was exploited to detect footprints of CTCF binding and to estimate the average nucleosome phasing distances in single cells.

2017-06-20 | GSE83882 | GEO

C42B NOMe-seq

Project description:C42B NOMe-seq

| PRJNA843048 | ENA

Genome-wide mapping of nucleosome positioning and DNA methylation within Individual DNA molecules

2012-09-12 | GSE40770 | 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

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