GEO DataSets

(Submitter supplied) 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). more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

25 Samples

Download data: WIG

(Submitter supplied) This experiment used ChIP-seq technology to create a genome-wide profile of histone marks in normal human pancreatic islets. In the current work we analyzed two histone marks associated with gene expression (H3K4me3, H3K4me1) and marks associated with gene repression (H3K27me3). Each mark was anayzed using samples obtained from four donors (n=4). Chromatin Immunoprecipitations (ChIPs) for histone marks were performed using specific anti-histone antibodies. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

21 Samples

Download data: BED, TXT

(Submitter supplied) Recent advances in the understanding of the genetics of type 2 diabetes (T2D) susceptibility have focused attention on the regulation of transcriptional activity within the pancreatic beta-cell. MicroRNAs (miRNAs) represent an important component of regulatory control, and have proven roles in the development of human disease and control of glucose homeostasis. We set out to establish the miRNA profile of human pancreatic islets and of enriched beta-cell populations, and to explore their potential involvement in T2D susceptibility. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17232

6 Samples

Download data: TXT

(Submitter supplied) Intrauterine growth restriction (IUGR) increases the risk of developing type 2 diabetes in adulthood. A rat model of IUGR induced by bilateral uterine artery ligation at day 18 of gestation, which reduces the blood supply and critical substrates to the fetus, was used to assess the alterations of genome-wide DNA methylation in IUGR islets. At 2 weeks of age, pancreatic islets were isolated and genomic DNA were extracted for TruSeq-HELP tagging assay. more...

Organism:

Rattus norvegicus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL22396

12 Samples

Download data: XLSX

(Submitter supplied) High-throughput sequencing of genomic regions isolated using FAIRE (Formaldehyde-assisted isolation of regulatory elements) from three purified pancreatic islet samples For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL9115 GPL3514

5 Samples

Download data: BED, PAIR, WIG

(Submitter supplied) DNA methylation profiling of whole blood using Illumina's Infinium HumanMethylation27 Beadchip array. The dataset encompasses profiles of 12 non-diabetic control blood donors and 12 type-2 diabetic (T2D) individuals.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

24 Samples

Download data: TXT

(Submitter supplied) Little is known about the contribution of the epigenome to the pathophysiology of type 2 diabetes (T2D). Here we have used genome-wide DNA methylation profiling to obtain the first comprehensive DNA methylation data set for human T2D pancreatic islets. Therefore, we analyzed the methylation profile of 27,578 CpG sites affiliated to more than 14,000 genes in 16 samples of pancreatic islets, 11 normal and 5 type 2-diabetic. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

16 Samples

Download data

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

206 Samples

Download data: CEL

(Submitter supplied) Pancreatic islet beta cell failure causes type 2 diabetes (T2D). The IMIDIA consortium has used a strategy entailing a stringent comparative transcriptomics analysis of islets isolated enzymatically or by laser microdissection from two large cohorts of non-diabetic (ND) and T2D organ donors (OD) or partially pancreatectomized patients (PPP). This work led to the identification of a signature of genes that were differentially expressed between T2D and ND regardless of the sample type (OD or PPP). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

103 Samples

Download data: CEL, TXT

(Submitter supplied) Pancreatic islet beta cell failure causes type 2 diabetes (T2D). The IMIDIA consortium has used a strategy entailing a stringent comparative transcriptomics analysis of islets isolated enzymatically or by laser microdissection from two large cohorts of non-diabetic (ND) and T2D organ donors (OD) or partially pancreatectomized patients (PPP). This work led to the identification of a signature of genes that were differentially expressed between T2D and ND regardless of the sample type (OD or PPP). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

103 Samples

Download data: CEL, TXT

(Submitter supplied) 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. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: BEDGRAPH

(Submitter supplied) Isoform quantification results for B6 mouse using Bowtie and RSEM.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

1 Sample

Download data: TSV

(Submitter supplied) Genetic variation at ~160 gene loci is associated with type 2 diabetes (T2D). Using an F2 mouse intercross segregating for T2D, we searched for a driver of GWAS gene expression and found that ~40% of the GWAS genes are regulated in trans by a locus on chromosome 2 in islets. We identified Nfatc2 as a candidate driver of GWAS gene expression. Overexpression of Nfatc2 induced β-cell proliferation in mouse and human islets. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

15 Samples

Download data: XLSX

(Submitter supplied) Identifying active regulatory elements and their characteristics is critical to understand gene regulatory mechanisms and subsequently better delineating biological mechanisms of complex diseases and traits. Studies have shown that active enhancers can be transcribed into enhancer RNA (eRNA). We identified actively transcribed elements in human pancreatic islets by performing cap analysis of gene expression (CAGE) across 70 islet samples. more...

Organism:

Rattus norvegicus; synthetic construct

Type:

Other

Platforms:

GPL27484 GPL23945

4 Samples

Download data: TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16686 GPL18460

12 Samples

Download data: CEL

(Submitter supplied) We performed ChIP-seq of PDX1 and H3K27ac on XM001 cells at PP stage

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18460

8 Samples

Download data: BED

(Submitter supplied) Objective: Homozygous loss-of-function mutations in the gene coding for the homeobox transcription factor (TF) PDX1 leads to pancreatic agenesis, whereas heterozygous mutations can cause Maturity-Onset Diabetes of the Young 4 (MODY4). Although the function of Pdx1 is well studied in pre-clinical models during insulin-producing β-cell development and homeostasis, it remains elusive how this TF controls human pancreas development by regulating a downstream transcriptional program. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

4 Samples

Download data: CEL

(Submitter supplied) Mouse strains like NZO and B6-ob/ob differ in their susceptibility to diet-induced diabetes. Comparison of the islet transcriptomes already revealed different biological processes, here we focused on alternative splicing events as one possible mechanism.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

10 Samples

Download data: XLSX

(Submitter supplied) Close to 50 genetic loci have been associated with type 2 diabetes (T2D), but they explain only 15% of the heritability. In an attempt to identify additional T2D genes, we analyzed global gene expression in human islets from 63 donors.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4337

Platform:

GPL6244

63 Samples

Download data: CEL

Analysis of pancreatic islets from type 2 diabetes (T2D) and non-diabetic cadaver donors. Glycemic control (HbA1c) levels also measured from the same individuals (normoglycemic: HbA1c < 6%; hyperglycemic: HbA1c ≥ 6%). Results provided insight into molecular basis of islet dysfunction in T2D.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 disease state, 23 other sets

Platform:

GPL6244

Series:

GSE38642

63 Samples

Download data: CEL