Ena-DATASET-WTCHG-03-02-2018-19:44:47:240-782 - samples
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ABSTRACT:
PROVIDER: EGAD00001003947 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:DNA from 10 human pancreatic islet samples was processed for Whole-genome Bisulphite Sequencing. The resulting libraries were sequenced on an Illumina Hiseq 2000 to generate 100bp paired-end read data. The resulting fastq.gz and mapped bam files were deposited.
| EGAD00001003946 | EGA
Project description:Insight on the understanding of the effect of maternal diabetes on embryonic nervous system development in embryos without neural tube defects. Control Group: Each sample (n) contained the RNA obtained by TRIZOL of a bulk of 30 prosencephalons (embryo day 12) of embryos from both sexes obtained from pregnant rats that were intraperitoneally injected with citrate buffer. n=3 Experimental group: Each sample (n) contained the RNA obtained by TRIZOL of A bulk of 30 prosencephalons (embryo day 12) of embryos from both sexes obtained from pregnant rats that were diabetic induced with an intraperitoneal administration of 50 mg/kg of streptozotocin. n=3 The sequence liberties were obtained through paired-end sequencing experiments. Codes for the files are as follows: Control E12: AM1_S1_R1_001.fastq.gz AM1_S1_R2_001.fastq.gz AM2_S2_R1_001.fastq.gz AM2_S2_R2_001.fastq.gz AM3_S3_R1_001.fastq.gz AM3_S3_R2_001.fastq.gz Diabetic E12: AM4_S4_R1_001.fastq.gz AM4_S4_R2_001.fastq.gz AM5_S5_R1_001.fastq.gz AM5_S5_R2_001.fastq.gz AM6_S6_R1_001.fastq.gz AM6_S6_R2_001.fastq.gz Were S = sample, R1 = sense sequencing, and R2 = antisense sequencing. Sequencing was performed on a NextSeq500 using the TruSeq HT kit from Illumina.
2025-05-15 | E-MTAB-15111 | biostudies-arrayexpress
Project description:There is growing evidence that transplantation of cadaveric human islets is an effective therapy for type 1 diabetes. However, gauging the suitability of islet samples for clinical use remains a challenge. We hypothesized that islet quality is reflected in the expression of specific genes. Therefore, gene expression in 59 human islet preparations was analyzed and correlated with diabetes reversal after transplantation in diabetic mice. Analysis yielded 262 differentially expressed probesets, which together predict islet quality with 83% accuracy. Pathway analysis revealed that failing islet preparations activated inflammatory pathways, while functional islets showed increased regeneration pathway gene expression. Gene expression associated with apoptosis and oxygen consumption showed little overlap with each other or with the 262 probeset classifier, indicating that the three tests are measuring different aspects of islet cell biology. A subset of 36 probesets surpassed the predictive accuracy of the entire set for reversal of diabetes, and was further reduced by logistic regression to sets of 14 and 5 without losing accuracy. These genes were further validated with an independent cohort of 16 samples. We believe this limited number of gene classifiers in combination with other tests may provide complementary verification of islet quality prior to their clinical use.
2017-09-14 | GSE75062 | GEO
Project description:The identification of cell surface markers specific to pancreatic islet cell subsets is important for both the study of islet biology and for investigating the pathophysiology of diseases in which these cell types are lost or damaged. Analysis of publicly available single-cell RNAseq data identified expression of LY6H specifically in the delta cells of the pancreas. This finding was confirmed using immunofluorescence analysis of histological sections of human pancreas, and flow cytometric analysis of human islet preparations. We found that expression of LY6H was restricted to pancreatic delta cells in both control and diabetic donors. Furthermore, we demonstrate that antibodies against LY6H can be used to isolate live delta cell populations from preparations of human islets. This study identified LY6H as a novel cell surface marker of human pancreatic delta cells – a finding that will aid in the identification and characterisation of this important cell type.
2025-04-23 | GSE264633 | GEO
Project description: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. We used Illumina small RNA sequencing to profile the miRNA fraction in three preparations each of primary human islets and of enriched beta-cells generated by fluorescence-activated cell sorting. In total, 366 miRNAs were found to be expressed (i.e. >100 cumulative reads) in islets and 346 in beta-cells; of the total of 384 unique miRNAs, 328 were shared. A comparison of the islet-cell miRNA profile with those of 15 other human tissues identified 40 miRNAs predominantly expressed (i.e. >50% of all reads seen across the tissues) in islets. Several highly-expressed islet miRNAs, such as miR-375, have established roles in the regulation of islet function, but others (e.g. miR-27b-3p, miR-192-5p) have not previously been described in the context of islet biology. As a first step towards exploring the role of islet-expressed miRNAs and their predicted mRNA targets in T2D pathogenesis, we looked at published T2D association signals across these sites. We found evidence that predicted mRNA targets of islet-expressed miRNAs were globally enriched for signals of T2D association (p-values <0.01, q-values <0.1). At six loci with genome-wide evidence for T2D association (AP3S2, KCNK16, NOTCH2, SCL30A8, VPS26A, and WFS1) predicted mRNA target sites for islet-expressed miRNAs overlapped potentially causal variants. In conclusion, we have described the miRNA profile of human islets and beta-cells and provide evidence linking islet miRNAs to T2D pathogenesis. Examination of the miRNA profiles in 3 preparations of isolated pancreatic islets and 3 preparations of FACS-enriched pancreatic beta-cells
2013-06-07 | E-GEOD-47720 | biostudies-arrayexpress
Project description:58 human clinical islet preparations were selected from the frozen biobank of the Cell Therapy Unit of Lille University Hospital. Total RNA was extracted and subjected to high-throughput sequencing on an Illumina platform. Transcriptomic profiles were subsequently analyzed and used for 2 studies : Type 2 diabetic vs. normoglycemic donors and NKX6.1-high vs. NKX6.1-low islets.
2026-03-22 | GSE324084 | GEO
Project description:An increasing demand for cell-based diabetes therapy could be met through xenotransplantation of adult porcine islets. Use of islet xenotranplantation on a large scale would require rigorous safety and quality control measures to maximize transplant success. Development of molecular tools to monitor porcine islet cellular responses to ischemic, osmotic, mechanical and oxidative stresses during islet cell processing and post-isolation culturing would aid the rational design of cytoprotective strategies aimed at improving transplant outcomes. In addition, gene expression signatures informative for islet quality could serve as an adjunct to physiological testing to establish the suitability of islet products for transplantation. Nine adult Landrace sows (2-3.5 y old, 249±27 kg) were sacrificed, the pancreases were dissected, and islet cells isolated as previously described [8]. Islet preparation purity was assessed by light microscopy after staining with diphenylthiocarbazone and ranged between 90-95% for the preparations used. Islet yield, based on islet equivalents (IEQ, number of islets standardized to 150 µm diameter), was estimated at 1930±520 per gram of pancreas tissue.Profiles of islet cells cultured under standard conditions were compared to islet cells cultured under stress conditions with elevated glucose (16.7 mM) or addition of inflammatory cytokines (IL-1ï¢, TNF-ï¡, and IFN-ï§), or both, for 48 hours.
2010-07-01 | E-GEOD-4744 | biostudies-arrayexpress
Project description:This GEO submission includes RNAseq raw data (fastq.gz) and processed data (using DESeq2) from samples obtained in the wild type and the pfd4 and 6x_pfd mutants
2020-12-22 | GSE138432 | GEO
Project description:We have developed an in vitro culture system that allows us to expand progenitor cells from human islet preparations and differentiate them into insulin-producing cells. We noticed however, that cultures from individual islet preparations had very heterogeneous outcomes, from good differentiation to almost none. We therefore speculated that our progenitor cell cultures contained different kinds of cells and that the true endocrine progenitor cells are present in the successful cultures, but not in the unsuccessful ones. To address this issue and to begin to identify markers for the true endocrine progenitor cells we compared global gene expression between a very successful culture (final insulin-expression 10% of islets) and an unsuccessful one (final insulin-expression 0%). We also included RNA from freshly isolated islets for control purposes. The cultures from donor A yielded substantial differentiation, while the cultures from donor B showed no successful differentiation.
2014-10-31 | E-MTAB-3050 | biostudies-arrayexpress