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| Status |
Public on Apr 06, 2019 |
| Title |
ATAC-seq on human pancreatic islets |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We have studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific TFs bind. Islet ATAC-seq peaks overlap with SNPs associated with T2D and with additional SNPs in LD with known T2D SNPs. There was enrichment of open chromatin regions near highly expressed genes in human islets.
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| Overall design |
Maps of open chromatin in human pancreatic islets from non-diabetic donors and donors with type 2 diabetes were generated by using ATAC-seq
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| Contributor(s) |
Bysani M, Agren R, Davegårdh C, Volkov P, Rönn T, Unneberg P, Bacos K, Ling C |
| Citation(s) |
31123324 |
| |
| Submission date |
Apr 05, 2019 |
| Last update date |
Jun 21, 2019 |
| Contact name |
Charlotte Ling |
| Organization name |
Lund University
|
| Department |
Department of Clinical Sciences
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| Lab |
Epigenetics & Diabetes
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| Street address |
Jan Waldenströms gata, 35
|
| City |
Malmö |
| ZIP/Postal code |
20502 |
| Country |
Sweden |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA531115 |
| SRA |
SRP191055 |
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