Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Retrieving high-resolution chromatin interactions and decoding enhancer regulatory potential in silico

ABSTRACT: Retrieving high-resolution chromatin interactions and decoding enhancer regulatory potential in silico

PROVIDER: PRJNA678980 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13074119_1.fastq.gz	Fastqsanger.gz
	SRR13074119_2.fastq.gz	Fastqsanger.gz
	SRR13074120_1.fastq.gz	Fastqsanger.gz
	SRR13074120_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Retrieving high-resolution chromatin interactions and decoding enhancer regulatory potential in silico

Project description:The advent of the chromosome conformation capture (3C) and related technologies has profoundly renewed our understaning of three-dimensional chromatin folding in mammalian nuclei. Alongside these experimental approaches, numerous computational tools for handling, normalizing, visualizing, and ultimately detecting interactions in 3C-type datasets are being developed. Here, we present Bloom, a comprehensive method for the analysis of 3C-type data matrices on the basis of Dirichlet process mixture models that addresses two important open issues. First, it retrieves occult interaction patterns from sparse data, like those derived from single-cell or “native” Hi-C experiments; thus, bloomed sparse data can now be used to study interaction landscapes at high-resolution. Second, it detects enhancer-promoter interactions with high sensitivity and inherently assigns an interaction frequency score (IFS) to each contact. Using enhancer perturbation data of different throughput, we show that IFS accurately quantifies the regulatory influence of each enhancer on its target promoter. As a result, Bloom allows decoding of complex regulatory landscapes by generating functionally-relevant enhancer atlases solely on the basis of 3C-type data.

2021-12-01 | GSE161636 | GEO

Decoding the transcriptome of denervated muscle at single-nucleus resolution

Project description:Decoding the transcriptome of denervated muscle at single-nucleus resolution

| PRJNA762034 | ENA

High-resolution mapping of multiway enhancer promoter interactions regulating pathogen detection

Project description:High-resolution mapping of multiway enhancer promoter interactions regulating pathogen detection

| PRJNA657630 | ENA

Decoding the endometrial niche of Asherman's syndrome at single-cell resolution

Project description:Decoding the endometrial niche of Asherman's syndrome at single-cell resolution

| PRJNA891357 | ENA

Decoding the transcriptome of calcified atherosclerotic plaque at single-cell resolution

Project description:Decoding the transcriptome of calcified atherosclerotic plaque at single-cell resolution

| PRJNA670178 | ENA

Genome-wide mapping of promoter-enhancer interactions with HiCap [HiCap]

Project description:Although the locations of promoters and enhancers have been identified in several cell types, we have yet limited information on their connectivity. We developed HiCap, which combines Hi-C with promoter sequence capture, to enable genome-wide identification of regulatory interactions with single-enhancer resolution. HiCap analyses of mouse embryonic stem cells (mESC) identified promoter-enhancer interactions predictive of gene expression change upon perturbation, opening up for genomic analyses of long-range gene regulation. HiCap was designed by combining Hi-C with with sequence capture (for all promoters) and carried out in mouse embryonic stem cells (mESC)

2015-07-06 | E-GEOD-60494 | biostudies-arrayexpress

MLL-AF4 cooperates with PAF1 and FACT to drive high density enhancer interactions in leukemia

Project description:Aberrant enhancer activation is a key mechanism driving oncogene expression in many cancers. While much is known about the regulation of larger chromosome domains in eukaryotes, the details of enhancer-promoter interactions remain poorly understood. Recent work suggests co-activators like BRD4 and Mediator have little impact on enhancer-promoter interactions. In leukemias controlled by the MLL-AF4 fusion protein, we use the ultra-high resolution technique Micro-Capture-C (MCC) to show that MLL-AF4 binding promotes broad, high-density regions of enhancer-promoter interactions at a subset of key targets. These enhancers are enriched for transcription elongation factors like PAF1C and FACT and loss of these factors abolishes enhancer-promoter contact. This work not only provides a new model for how MLL-AF4 is able to drive high levels of transcription at key genes in leukemia, but also suggests a more general model linking enhancer-promoter crosstalk and transcription elongation.

2023-08-18 | PXD043920 | Pride

Decoding the endometrial niche of Asherman's syndrome at single-cell resolution [organoids]

Project description:Decoding the endometrial niche of Asherman's syndrome at single-cell resolution [organoids]

| PRJNA895089 | ENA

Genome-wide mapping of promoter-enhancer interactions with HiCap [RNA-seq]

2015-07-06 | E-GEOD-60493 | biostudies-arrayexpress

Genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

Project description:The enhancer-promoter looping model, in which enhancers activate their target genes via physical contact, has been the dominant hypothesis in the field for decades. However, a systematic testing of this hypothesis has not been conducted, primarily due to the absence of suitable experimental techniques. In this study, we present a new MNase-based proximity ligation method called MChIP-C, allowing for the measurement of protein-mediated chromatin interactions at single-nucleosome resolution on a genome-wide scale. By applying MChIP-C to study H3K4me3 promoter-centered interactions in K562 cells, we found that it had greatly improved resolution and sensitivity compared to restriction endonuclease-based C-methods. This allowed us to identify EP300 histone acetyltransferase and the SWI/SNF remodelling complex as potential candidates for establishing and/or maintaining enhancer-promoter interactions. Finally, leveraging data from published CRISPRi screens, we found that most functionally-verified enhancers do physically interact with their cognate promoters, supporting the enhancer-promoter looping model.

2023-12-24 | GSE225087 | 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