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

f43ad0e6-8478-4fa8-b474-8da7521749d1 - samples

Project description:4 Promoter-Capture Hi-C datasets of human pancreatic islets from 4 human islet donors

| EGAD00001005206 | EGA

Gene expression in 832/13 INS1 beta-cells transduced with lentiviral vector conferring expression of GFP or Pax5

Project description:We found PAX5 to be overexpressed in human pancreatic islets of donors from donors with type 2 diabetes compared to islets from non-diabetic individuals. Functional follow-up showed that Pax5 overexpression in rat clonal beta-cells (832/13 INS1) results in impaired insulin secretion. Microarrays were used to investigate if overexpression of Pax5 alters the gene expression profile of 832/13 INS1 beta-cells.

2023-01-11 | GSE211310 | GEO

ATAC-seq on human pancreatic islets

Project description:ATAC-seq on human pancreatic islets

| PRJNA531115 | ENA

18c3c6ae-3626-41c0-8f64-eeeebe56788b - samples

Project description:14 ChIP-Seq datasets of H3K27ac in human pancreatic islets from 14 donors, where islets were treated in high (11mM) glucose conditions. Samples IDs HI-129, HI-130, HI-131, HI-132, HI-135, HI-137 and HI-152 were also cultured in low glucose conditions.

| EGAD00001005204 | EGA

Chromatin accessibility (ATAC-seq) of human acute leukemias and healthy donors

Project description:ATAC-seq of 79 primary samples obtained from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). Moreover, ATAC-seq of CD34+ HSPCs from 3 healthy donors are included. ATAC-seq was performed as described (Buenrostro et al., 2013) with a modification in the lysis buffer to reduce mitochondrial DNA contamination. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011050 (dataset).

2023-08-31 | E-MTAB-13118 | biostudies-arrayexpress

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