Study

Human islet 3D chromatin maps provide insights into type 2 diabetes

Study ID Alternative Stable ID Type
EGAS00001002917 Other

Study Description

The transcriptional output of each cell type is controlled by thousands of enhancers, many of which contain genetic risk variants for common diseases such as type 2 diabetes (T2D). To gain insight into how enhancer variation influences diabetes risk, we created promoter capture Hi-C maps in human pancreatic islets. This linked diabetes-associated islet enhancers with their target genes, often located hundreds of kilobases away. We identified hubs that show spatial and functional connections between enhancersand target genes related to islet function and diabetes. We demonstrate that genetic variants distributed across hub enhancers have a major impact on T2D heritability, and use this knowledge to identify individuals in whom islet regulatory variation has a prominent role in T2D risk. Our results demonstrate the importance of 3D chromatin architecture for molecular interpretation of T2D genetic association signals, and define genomic spaces that harbor a distinct component of the T2D polygenic burden.

Study Datasets 10 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001005201
13 ATAC-Seq datasets of human pancreatic islets from 13 donors
Illumina HiSeq 2500 13
EGAD00001005202
6 ChIP-Seq datasets of Mediator in human pancreatic islets from 6 donors
Illumina HiSeq 2500 6
EGAD00001005203
3 ChIP-Seq datasets of Cohesin in human pancreatic islets from 3 donors
Illumina HiSeq 2500 3
EGAD00001005204
14 ChIP-Seq datasets of H3K27ac in human pancreatic islets from 14 donors, where islets were treated in high (11mM) glucose conditions. Samples IDs HI-129, HI-130, HI-131, HI-132, HI-135, HI-137 and HI-152 were also cultured in low glucose conditions.
Illumina Genome Analyzer IIx,Illumina HiSeq 2500 14
EGAD00001005205
7 H3K27ac ChIP-Seq datasets from 7 donors where islets were treated in low (4mM) glucose conditions.
Illumina HiSeq 2500 7
EGAD00001005206
4 Promoter-Capture Hi-C datasets of human pancreatic islets from 4 human islet donors
Illumina HiSeq 2500 4
EGAD00001005207
7 RNA-Seq datasets in human pancreatic islets from 7 donors, where islets were treated in high (11mM) glucose conditions
Illumina HiSeq 2500 7
EGAD00001005208
7 RNA-Seq datasets in human pancreatic islets from 7 donors, where islets were using low (4mM) glucose conditions.
Illumina HiSeq 2500 7
EGAD00001005209
Input dataset of human islets. To be used in conjuction with Cohesin and Mediator ChIP-Seq datasets.
Illumina HiSeq 2500 1
EGAD00001005210
2 Circular chromosome conformation capture (4C-Seq) datasets of the human beta cell line EndoC-bh1.
Illumina HiSeq 2500 1

Who archives the data?

There are no publications available