Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [10x ATAC + GEX Multiome]

ABSTRACT: We developed a strategy (Perturb-Multiome) to couple highly-efficient pooled CRISPR-mediated perturbation of master transcription factors in differentiating primary human hematopoietic cells with joint single-cell gene expression and chromatin accessibility profiling. This approach enabled the reconstruction of transcription factor-dependent gene regulatory networks throughout hematopoietic differentiation. Ultimately, we integrated GWAS datasets to explore the heritability of blood phenotypes explained by these identified transcription-factor regulatory networks.

ORGANISM(S): Homo sapiens

PROVIDER: GSE274113 | GEO | 2025/04/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [10x ATAC + GEX Multiome]

Project description:Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [10x ATAC + GEX Multiome]

| PRJNA1144976 | ENA

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [PRO-Seq]

Project description:We developed a strategy to couple highly-efficient pooled CRISPR-mediated perturbation of key master hematopoietic transcription factors in differentiating primary human hematopoietic cells with joint single-cell gene expression and chromatin accessibility profiling to enable the reconstruction of transcription factor-dependent gene regulatory networks throughout primary hematopoietic differentiation.

2025-04-03 | GSE274110 | GEO

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [PRO-Seq]

Project description:Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes [PRO-Seq]

| PRJNA1144972 | ENA

Spatially resolved multiomics of human cardiac niches - Multiome GEX

Project description:Using Multiome and previously published sc/snRNA-seq data, we studied eight anatomical regions of the human heart including left and right ventricular free walls (LV and RV), left and right atria (LA and RA), left ventricular apex (AX), interventricular septum (SP), sino-atrial node (SAN) and atrioventricular node (AVN). For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors and cell-cell interactions. We map the identified cells to spatial transcriptomic data to discover cellular niches within the eight regions of the heart.

2023-06-13 | E-MTAB-12916 | biostudies-arrayexpress

Single-nucleus multiome (RNA+ATAC) sequencing of the axolotl pallium

Project description:In order to understand the genomic and transcriptomic variability of the axolotl pallium, as well as reconstruct their intrinsic gene regulatory networks, we performed single-nucleus multiome sequencing (RNA and open chromatin) of whole axolotl pallium.

2022-07-20 | E-MTAB-11666 | biostudies-arrayexpress

Spatially resolved multiomics of human cardiac niches - Multiome GEX

Project description:Spatially resolved multiomics of human cardiac niches - Multiome GEX

| PRJEB61891 | ENA

Baf155 establishes chromatin priming to promote hematopoietic regeneration and function [single cell multiome - ATAC + GEX]

Project description:Chromatin priming promotes cell type-specific gene expression, lineage differentiation, and development. The mechanism of chromatin priming has not been well understood. Mouse hematopoietic stem and progenitor cells (HSPCs) lacking the Baf155 subunit of the BAF (BRG1/BRM associated factor) chromatin-remodeler produced a significantly reduced number of mature blood cells, leading to a failure of hematopoietic regeneration upon transplantation and 5-FU injury. Baf155 deficient HSPCs, while showing impaired mature blood cell production, generated a higher frequency of myeloid cells with fewer B and CD8+ T cells at homeostasis, supporting a more immune-suppressive tumor microenvironment and enhanced tumor growth. Single-nuclei multi-omic analysis revealed that Baf155 deficient HSPCs failed to establish accessible chromatin and levels of lineage-specific transcripts were considerably lower. Regions that showed a substantial loss in chromatin accessibility were enriched for enhancers and binding motifs for hematopoietic lineage-specific transcription factors. Our study provides a fundamental mechanistic understanding of the role of Baf155 in establishing chromatin priming with functional consequences in regeneration or tumor immunity.

2024-07-09 | GSE240583 | GEO

Multiome analysis (ATAC + Gene Expression (GEX)) of SUN1 knockout and control CT26 tumors grown in syngeneic mouse model

Project description:T cell infiltration is essential for immune checkpoint inhibitors to be effective in treating solid cancers. Through a bioinformatic pipeline, we identified a target gene SUN1 that might relate to modulating immune cell infiltration and immune response. Thus, we generated one Sun1_knockout CT26 cell line (Sun1_KO) using CRISPR-Cas9. By performing multiome single nuclei sequencing using tumors grown in syngeneic model, we set out to understand how mouse Sun1 can affect the regulatory network in tumor cells in vivo.

2024-03-29 | GSE262237 | GEO

Baf155 establishes chromatin priming to promote hematopoietic regeneration and function [single cell multiome - ATAC + GEX]

Project description:Baf155 establishes chromatin priming to promote hematopoietic regeneration and function [single cell multiome - ATAC + GEX]

| PRJNA1004272 | ENA

Multiome experiment from GLI3 KO brain organoids

Project description:To study the effect of GLI3 knockout on early brain organoid development, we collected single-cell multiome data from 18 day old brain organoids

2022-08-25 | E-MTAB-12002 | biostudies-arrayexpress

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