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Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism [RNA-seq]

ABSTRACT: Here we harnessed the potential of RNA sequencing in 89 human pancreatic islet donors to identify genes and exons regulated in this relevant tissue for T2D.

ORGANISM(S): Homo sapiens

PROVIDER: GSE50244 | GEO | 2014/07/17

SECONDARY ACCESSION(S): PRJNA217347

REPOSITORIES: GEO

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Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism [RNA-seq]

Project description:Here we harnessed the potential of RNA sequencing in 89 human pancreatic islet donors to identify genes and exons regulated in this relevant tissue for T2D. mRNA profiles of 89 human pancreatic islet donors having different levels of blood glucose (HbA1c) with and without T2D. The data was generated by deep sequencing using Illumina HiSeq 2000.

2014-07-17 | E-GEOD-50244 | biostudies-arrayexpress

Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism [expression array]

Project description:Here we harnessed the potential of expression arrays in 89 human pancreatic islet donors (different levels of blood glucose (HbA1c)) to identify genes regulated in this relevant tissue for type 2 diabetes (T2D). Islets from cadaver donors were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChipM-BM-. Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.

2014-07-17 | E-GEOD-50397 | biostudies-arrayexpress

Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism [expression array]

2014-07-17 | GSE50397 | GEO

ATAC-seq on human pancreatic islets

Project description: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.

2019-04-06 | GSE129383 | GEO

Expression data from human pancreatic islets

Project description: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. Islets from cadaver donors (54 non-diabetic and 9 diabetic) were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChipM-BM-. Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.

2012-07-05 | E-GEOD-38642 | biostudies-arrayexpress

Single-cell chromatin landscapes of human islets in normoglycemia, prediabetes and type 2 diabetes

Project description:In this study, we used single cell nucleus ATAC-seq (snATAC-seq) to profile 218,973 islet cells from 34 individuals, including islets from non-diabetic, pre-diabetic and type 2 diectic (T2D) donors. We characterize changes in regulatory programs of islet cell types in T2D progression, describe the relationship of these programs to genetic risk for T2D, and use allelic imbalance mapping to define cell type-specific functions for candidate T2D causal variants.

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Single-cell multiome (ATAC and RNA) landscapes of human islets in normoglycemia, prediabetes and type 2 diabetes

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Expression data from human pancreatic islets

Project description:A gene co-expression network analysis has been conducted to identify T2D-associated gene modules. Donors 1-48 were used for the initial analysis and donors 49-80 for the replication and were normalized separately in this study Islets from cadaver donors (57 non-diabetic and 20 diabetic) were provided by the Nordic Islet Transplantation Programme (www.nordicislets.org), Uppsala University. The microarrays were performed using GeneChipM-BM-. Human Gene 1.0 ST whole transcript according to Affymetrix standard protocol.

2012-10-23 | E-GEOD-41762 | biostudies-arrayexpress

MicroRNA expression profiling of human pancreatic islets reveals microRNAs with altered expression due to glyceamic status

Project description:Global microRNA (miRNA) profiling was performed in 18 human islet donors using Exiqon’s LNA (locked nucleic acid)-based array platform. Donors were divided into three groups according to their HbA1c levels and type-2 diabetes diagnosis (normal glucose tolerance - NGT, impaired glucose tolerance - IGT, diagnosed with type-2 diabetes-T2D). To identify miRNAs with altered expression due to glyceamic status, donors were matched for age, gender and BMI and differential expression analysis was performed in 7 NGT vs 7 IGT/T2D donors using Significance Analysis of Microarrays (SAM) based on False Discovery Rate (FDR) statistics.

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Project description:In this study, we achieved integrated transcriptomic and proteomic profiles of GK islets in a time-course fashion at different stages of T2D. Subsequent bioinformatics analysis revealed the chronological order of T2D-related molecular events during the deterioration of pancreatic islets. Our large quantitative dataset provide a valuable resource to obtain a comprehensive picture of the mechanisms responsible for islet dysfunction and to identify potential interventions to prevent beta-cell failure in human T2D.

2017-06-02 | PXD004709 | Pride

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