Single-nucleus and single-cell RNA-sequencing of human pancreatic islets
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ABSTRACT:
PROVIDER: PRJNA856476 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptomics is frequently used to interrogate alterations in cultured human islet cells using single-cell RNA-sequencing. We introduce single-nucleus RNA-sequencing as an alternative approach for investigating human islets.
2022-07-10 | GSE207632 | GEO
Project description:Using single-nucleus RNA-sequencing to interrogate transcriptomic profiles of archived human pancreatic islets
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Project description:Human pancreatic islets, including insulin secreting beta-cells are a major focus of transplantation strategies aimed at identifying new therapeutic approaches to counteract hyperglycemia in patients with diabetes. Identifying the transcriptomic signature of human islet cells provides insights into regulatory pathways that can be harnessed for planning therapeutic strategies. In this context, single-cell RNA-sequencing (scRNA-seq) has been used mostly in vitro. However, in experimental human islet transplantation models the small amount of tissue is principally used for immunostaining and poses a challenge in performing ‘omics’ studies that provide unbiased information. To circumvent this limitation, we report the use of single nucleus RNA-sequencing (snRNA-seq) on frozen/archived human islet grafts, to define the transcriptomic signature of islet cells preserved after in vivo studies. Interrogating nuclear RNA, we were able to successfully identify all islet endocrine cells, obtain adequate coverage of genes and define molecular pathways that are important for studying human islet cell biology (e.g. cell cycle, apoptosis, insulin secretion). Intersecting our nuclear transcriptomic output with publicly available single-cell RNA-seq datasets, revealed ~90% overlap of the detected genes. In conclusion, we propose that snRNA-seq represents a reliable strategy to probe transcriptomic profiles of fresh or archived transplanted human islets.
2021-07-09 | GSE150212 | GEO
Project description:Human pancreatic islets methylation array
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Project description:LC-IMS-MS data of single mouse pancreatic islets.
2022-11-08 | MSV000090670 | GNPS
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:Filter-aided sample preparation (FASP) is widely used in bottom-up proteomics for tryptic digestion. However, the sample recovery yield of this method is limited by the amount of starting material. While ~100 ng of digested protein sample is sufficient for thorough protein identification, proteomic information gets lost after digestion of samples with a protein content < 10 µg due to incomplete peptide recovery from the filter. By reducing the filter area as well as the volumes of all reagents, we developed and optimized a well-plate µFASP device and protocol that is suitable for ~1 µg protein sample. In 1 µg of HeLa digest, we identified 1295 ± 10 proteins with our method followed by analysis with liquid chromatography–mass spectrometry. In contrast, only 524 ± 5 proteins were identified with the standard FASP protocol while 1395 ± 4 proteins were identified in 20 µg after standard FASP as a benchmark. Furthermore, we used our method to conduct a combined peptidomic and proteo-mic study of single islets of Langerhans. Here, we separated neuropeptides from single islets as effluents from a ⌀ 1 mm molecular cut-off filter and digested the remaining on-filter proteins for bottom-up proteomic analysis. Our results indicate inter-islet heterogeneity for expression of proteins involved in glucose catabolism, pancreatic hormone processing and secreted peptide hormones. We consider our method to provide a useful tool for proteomic characterization of samples where biological material is scarce.
2022-04-01 | PXD029039 | Pride
Project description:Sin3A mutant pancreatic islets
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Project description:ATAC-seq on human pancreatic islets
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Project description: Not available
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