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Series GSE23784 Query DataSets for GSE23784
Status Public on Nov 02, 2010
Title Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Identifying cis-regulatory elements is important to understand how human pancreatic islets modulate gene expression in physiologic or pathophysiologic (e.g., diabetic) conditions. We conducted genome-wide analysis of DNase I hypersensitive sites, histone H3 lysine methylation marks (K4me1, K4me3, K79me2), and CCCTC factor (CTCF) binding in human islets. This identified ~18,000 putative promoters (several hundred novel and islet-active). Surprisingly, active promoter marks were absent at genes encoding islet-specific hormones, suggesting a distinct regulatory mechanism. Of 34,039 distal (non-promoter) regulatory elements, 47% are islet-unique and 22% are CTCF-bound. These findings present a global snapshot of the human islet epigenome and should provide functional context for non-coding variants emerging from genetic studies of T2D and other pancreatic islet disorders.
Overall design Three different islet samples were tested for DNase I hypersensitivity by DNase-Seq. Five different primary pancreatic islet samples were evaluated for several chromatin modifications (H3K4me3, H3K4me1, H3K79me2) by ChIP-seq. One islet sample was evaluated for CTCF binding via ChIP-seq, All ChIP-seq samples have both non-specific IP (GFP) and input DNA controls.
Contributor(s) Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ, Margulies EH, Boehnke M, Furey TS, Crawford GE, Collins FS
Citation(s) 21035756, 23997652
Submission date Aug 24, 2010
Last update date Aug 13, 2019
Contact name Francis S Collins
Organization name NHGRI
Department Genome Technology Branch
Lab Molecular Genetics Section
Street address 1 Center Drive, Rm 126
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (25)
GSM586869 Islet1_K4me3
GSM586870 Islet2_GFP
GSM586871 Islet2_Input
SRA SRP003499
BioProject PRJNA130725

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Supplementary file Size Download File type/resource
GSE23784_RAW.tar 888.6 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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