Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [scATAC]

ABSTRACT: Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [scATAC]

PROVIDER: PRJNA893558 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22020243_1.fastq.gz	Fastqsanger.gz
	SRR22020243_2.fastq.gz	Fastqsanger.gz
	SRR22020244_1.fastq.gz	Fastqsanger.gz
	SRR22020244_2.fastq.gz	Fastqsanger.gz
	SRR22020245_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [scATAC]

Project description:Cis-regulatory elements (CREs) are bound by diverse chromatin-associated proteins, cooperate to establish gene expression, and change in structure over time to alter cell fate and function1–3. Here, we develop a footprinting framework that uses deep learning to correct Tn5 sequence bias, improving accuracy and reducing false positives. This framework additionally identifies the interaction of DNA with objects of various sizes. Using these ‘multi-scale footprints’ we find that transcription factor (TF) binding occurs at well-defined distances from nucleosomes. Further, we demonstrate that multi-scale footprints, which include the positions of nucleosomes, enable more accurate inference of TF binding. Using multi-scale footprinting with single-cell multi-omics, we discover wide-spread structural and functional changes of CREs across hematopoiesis, wherein nucleosomes slide, expose DNA for TF binding, and promote gene expression. Finally, we apply this single-cell and footprint approach to characterize age-associated structural changes to CREs within hematopoietic stem cells and identify a spectrum of cells harboring age-associated changes to the epigenome. Interestingly, we find extensive changes to the structure of CREs upon aging, with many age-associated changes altering CRE structure while preserving overall accessibility. Collectively, we reveal the dynamics and functional importance of CRE structure, highlighting changes to gene regulation at single-cell and single-base-pair resolution.

2023-03-29 | GSE216406 | GEO

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [BAC]

2023-03-29 | GSE216403 | GEO

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [scRNA-Seq]

2023-03-29 | GSE216405 | GEO

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [SHARE-Seq]

2023-03-29 | GSE216404 | GEO

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [Human BMMC ATAC]

2023-03-29 | GSE216462 | GEO

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [Human BMMC RNA]

2023-03-29 | GSE216461 | GEO

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [BAC]

Project description:Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [BAC]

| PRJNA893555 | ENA

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [scRNA-Seq]

Project description:Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [scRNA-Seq]

| PRJNA893557 | ENA

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [SHARE-Seq]

Project description:Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [SHARE-Seq]

| PRJNA893556 | ENA

Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [Human BMMC RNA]

Project description:Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [Human BMMC RNA]

| PRJNA893664 | 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