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Interpreting type 1 diabetes risk with genetics and single cell epigenomics

ABSTRACT: Interpreting type 1 diabetes risk with genetics and single cell epigenomics

PROVIDER: PRJNA685127 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13252428_1.fastq.gz	Fastqsanger.gz
	SRR13252428_2.fastq.gz	Fastqsanger.gz
	SRR13252429_1.fastq.gz	Fastqsanger.gz
	SRR13252429_2.fastq.gz	Fastqsanger.gz
	SRR13252430_1.fastq.gz	Fastqsanger.gz

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Interpreting type 1 diabetes risk with genetics and single cell epigenomics

Project description:Genetic risk variants identified in genome-wide association studies (GWAS) of complex disease are primarily non-coding, and translating risk variants into mechanistic insight requires detailed gene regulatory maps in disease-relevant cell types. Here, we combined a GWAS of type 1 diabetes (T1D) in 520,580 samples with candidate cis-regulatory elements (cCREs) in pancreas and peripheral blood mononuclear cell types defined using single nucleus ATAC-seq (snATAC-seq) of 131,554 nuclei. T1D risk variants were enriched in cCREs active in T cells and additional cell types, including acinar and ductal cells of the exocrine pancreas. Risk variants at multiple T1D signals overlapped exocrine-specific cCREs linked to genes with exocrine-specific expression. At the CFTR locus, T1D risk variant rs7795896 mapped in a ductal-specific cCRE which regulated CFTR, and the risk allele reduced transcription factor binding, enhancer activity and CFTR expression in ductal cells. These findings support a role for the exocrine pancreas in T1D pathogenesis and highlight the power of large-scale GWAS and single cell epigenomics for understanding the cellular origins of complex disease.

2021-03-15 | GSE163160 | GEO

Discovering human diabetes-risk gene function with genetics and physiological assays

Project description:Discovering human diabetes-risk gene function with genetics and physiological assays

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Discovering human diabetes-risk gene function with genetics and physiological assays

Project description:To delineate the effects of BCL11A (a type 2 diabetes risk gene) in human beta cell function we knockdown BCL11A in primary human beta cells and generated and sequenced RNA-seq libraries from 4 human donors

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Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk

Project description:Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type-specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell-derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.

2021-01-14 | GSE160474 | GEO

Single-cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk [RNA-seq]

2021-01-14 | GSE160473 | GEO

Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk [snATAC-seq]

Project description:Single-nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq) creates new opportunities to dissect cell type–specific mechanisms of complex diseases. Since pancreatic islets are central to type 2 diabetes (T2D), we profiled 15,298 islet cells by using combinatorial barcoding snATAC-seq and identified 12 clusters, including multiple alpha, beta and delta cell states. We cataloged 228,873 accessible chromatin sites and identified transcription factors underlying lineage- and state-specific regulation. We observed state-specific enrichment of fasting glucose and T2D genome-wide association studies for beta cells and enrichment for other endocrine cell types. At T2D signals localized to islet-accessible chromatin, we prioritized variants with predicted regulatory function and co-accessibility with target genes. A causal T2D variant rs231361 at the KCNQ1 locus had predicted effects on a beta cell enhancer co-accessible with INS and genome editing in embryonic stem cell–derived beta cells affected INS levels. Together our findings demonstrate the power of single-cell epigenomics for interpreting complex disease genetics.

2021-01-14 | GSE160472 | GEO

Single cell chromatin accessibility identifies pancreatic islet cell type- and state-specific regulatory programs of diabetes risk [Hi-C]

2021-01-14 | GSE163610 | GEO

Pancreatic islet epigenomics reveals enhancer clusters that are enriched in Type 2 diabetes risk variants

Project description:Pancreatic islet epigenomics reveals enhancer clusters that are enriched in Type 2 diabetes risk variants

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Type 1 Diabetes Genetics Consortium (T1DGC) ImmunoChip Study

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