Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-omics gene regulatory network analysis of resting and stimulated PBMCs

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE178431 | GEO | 2022/06/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [scATAC-seq]

Project description:Cells require coordinated control over gene expression changes when responding to environmental stimuli. Recent advancements in single-cell technologies have enabled studies of regulatory dynamics associated with cellular perturbation response in immune cells. However, associating these changes to underlying differences in epigenetic regulation through integration of multi-omic data has not been achieved at single-cell resolution. Here, we apply single-cell ATAC-seq (scATAC-seq) and scRNA-seq to assay chromatin accessibility and gene expression in resting and stimulated human blood cells. Collectively, we generate ~91,000 high-coverage single-cell profiles, allowing us to probe the cis-regulatory landscape of immunological response across cell types, stimuli and time. Advancing tools to integrate multiomic data, we connect distal cis-regulatory elements to genes, identifying key regulatory hubs associated with immune signaling and stress response. Subsequently, we design FigR - a method to infer gene regulatory networks (GRNs) to identify candidate TF regulators across single cells. Importantly, construction of a GRN using stimulus response data identifies TF regulatory activity associated with genetic variants in inflammatory diseases. Lastly, we assess the time-dependent regulatory dynamics of immune stimulation, where we find that cells alter chromatin accessibility prior to productive gene expression, a process occurring at time scales of minutes. Extending this concept of chromatin-mediated priming, and incorporating regulatory relationships defined by FigR, we detect a rare subpopulation of monocytes marked by a primed chromatin state predictive of enhanced immunological response. Overall, we build upon computational tools for GRN construction and demonstrate the utility of GRNs for analysis of multi-omic single cell data.

2022-06-20 | GSE178428 | GEO

Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [stimulation scRNA-seq]

2022-06-20 | GSE178429 | GEO

Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [PBMC isolate scRNA-seq]

2022-06-20 | GSE178430 | GEO

Multi-omics gene regulatory network analysis of resting and stimulated PBMCs

Project description:Multi-omics gene regulatory network analysis of resting and stimulated PBMCs

| PRJNA738944 | ENA

Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [scATAC-seq]

Project description:Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [scATAC-seq]

| PRJNA738945 | ENA

Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [stimulation scRNA-seq]

Project description:Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [stimulation scRNA-seq]

| PRJNA738946 | ENA

Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [PBMC isolate scRNA-seq]

Project description:Multi-omics gene regulatory network analysis of resting and stimulated PBMCs [PBMC isolate scRNA-seq]

| PRJNA738947 | ENA

Single nucleus multi-omics regulatory atlas of the murine pituitary

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-02-23 | GSE151962 | GEO

Multi-level omics analysis of dystrophin loss and therapeutic restoration in a murine model

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-09-24 | E-GEOD-64420 | biostudies-arrayexpress

Integrated multi-omics analysis

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-09-05 | GSE254297 | 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