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Series GSE129383 Query DataSets for GSE129383
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
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.
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
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
Lab Epigenetics & Diabetes
Street address Jan Waldenströms gata, 35
City Malmö
ZIP/Postal code 20502
Country Sweden
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (15)
GSM3712139 Sample 1
GSM3712140 Sample 2
GSM3712141 Sample 3
BioProject PRJNA531115
SRA SRP191055

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Supplementary file Size Download File type/resource
GSE129383_RAW.tar 5.8 Gb (http)(custom) TAR (of BEDGRAPH)
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Raw data are available in SRA
Processed data provided as supplementary file

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