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Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells

ABSTRACT: Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells

PROVIDER: PRJNA594953 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10669617_1.fastq.gz	Fastqsanger.gz
	SRR10669617_2.fastq.gz	Fastqsanger.gz
	SRR10669618_1.fastq.gz	Fastqsanger.gz
	SRR10669618_2.fastq.gz	Fastqsanger.gz
	SRR10669619_1.fastq.gz	Fastqsanger.gz

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Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [RNA-seq]

Project description:Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [RNA-seq]

| PRJNA594959 | ENA

Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ATAC-seq]

Project description:Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ATAC-seq]

| PRJNA594958 | ENA

Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [HiChIP-seq]

Project description:Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [HiChIP-seq]

| PRJNA594960 | ENA

Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ChIP-seq]

Project description:Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ChIP-seq]

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Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [HiChIP-seq]

Project description:Despite overwhelming evidence supporting the role of genetics in susceptibility tocomplex diseases, such as autoimmune disorders, a fundamental unresolved questionis whether large numbers of sequence variants with small effect sizes can alter thespatial genome organization. Here, we provide the first report on the reconfiguration ofthe 3D genome due to nucleotide differences associated with type 1 diabetes, anautoimmune disorder. We show that the chromatin organization at T cell identity genesis identical between diabetes-susceptible and diabetes-resistant mouse strains despitethousands of sequence polymorphisms, suggesting that these loci are epigeneticallyresilient to genetic variation. However, molecular and optical mapping of genomefolding demonstrate that diabetes risk-conferring loci coalesce into close spatialproximity in T cells of diabetes-susceptible mice, forming regulatory cliques, andresulting in aberrant gene expression. Our data uncover 3D chromatin architecture asa new dimension in understanding complex diseases

2020-02-11 | GSE141847 | GEO

Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ChIP-seq]

2020-02-11 | GSE141846 | GEO

Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [ATAC-seq]

2020-02-11 | GSE141845 | GEO

Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells [RNA-seq]

2020-02-11 | GSE141852 | GEO

Genetic Variations in Type 1 Diabetes Reconfigure the 3D Chromatin Organization of T Cells

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

2020-02-11 | GSE141853 | GEO

Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells

Project description:The organization of mammalian genomes within the nucleus features a complex, multiscale three-dimensional (3D) architecture. The functional significance of these 3D genome features, however, remains largely elusive due to limited single-cell technologies that can concurrently profile genome organization and transcriptional activities. Here, we report GAGE-seq, a highly scalable, robust single-cell co-assay that simultaneously measures 3D genome structure and transcriptome within the same cell. Employing GAGE-seq on mouse brain cortex and human bone marrow CD34+ cells, we comprehensively characterized the intricate relationships between 3D genome and gene expression. We found that these multiscale 3D genome features collectively inform cell type-specific gene expressions, hence contributing to defining cell identity at the single-cell level. Integration of GAGE-seq data with spatial transcriptomic data revealed in situ variations of the 3D genome in mouse cortex. Moreover, our observations of lineage commitment in normal human hematopoiesis unveiled notable discordant changes between 3D genome organization and gene expression, underscoring a complex, temporal interplay at the single-cell level that is more nuanced than previously appreciated. Together, GAGE-seq provides a powerful, cost-effective approach for interrogating genome structure and gene expression relationships at the single-cell level across diverse biological contexts.

2024-03-27 | GSE238001 | GEO

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