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RNAseq data for EndoC-βH1 treated with CM from omental stromal cells cultured either in the absence or presence of TNF-α or differentiated into adipocytes

ABSTRACT: RNAseq data for EndoC-βH1 treated with CM from omental stromal cells cultured either in the absence or presence of TNF-α or differentiated into adipocytes

PROVIDER: PRJNA766450 | ENA |

REPOSITORIES: ENA

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RNAseq data for EndoC-βH1 treated with CM from omental stromal cells cultured either in the absence or presence of TNF-α or differentiated into adipocytes

Project description:We used an in vitro model to study the paracrine effect of stromal cells isolated from omental adipose tissue at different stages of differentiation and inflammation on the beta cell lines EndoC-βH1 through the use of conditioned media. We show that the expression of beta cells markers decreased and dedifferentiation markers increased when beta cells were cultured in conditioned medium derived from omental stromal cells. We report that stromal cells with a high pro-inflammatory profile had the most severe impact. By using RNAseq, we showed the stimulation of several signaling pathways such as STAT3, SMAD2 and RELA, as well as the downregulation of genes involved in lipogenesis and cholesterol synthesis.

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Genome-wide maps of chromatin state in EndoC-βH1 Cells

Project description:We report the actively transcribed chromatin regions in EndoC-βH1 Cells that are associated with histone H3 lysine 27 acetylation mark.

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Characterization of EndoC-BH5 a novel human pancreatic beta cell line. Comparative expression profile with EndoC-BH1 and effect of stimulation with Interferon gamma and interleukin 1b.

Project description:We have developped a novel human pancreatic beta cell line: EndoC-βH5. EndoC-βH5 cells are ready-to-use and storable cells with physiological insulin secretion. EndoC-βH5 cells were generated by integrative gene transfer of immortalizing transgenes hTERT and SV40 large T along with Herpes Simplex Virus-1 thymidine kinase into human fetal pancreas. Immortalizing transgenes were removed after amplification using CRE activation and remaining non-excized cells eliminated using ganciclovir. Resulting cells were distributed as ready to use EndoC-βH5 cells. We performed comparative transcriptome analysis with EndoC-βH1 cells , extensive functional and immunological assays. RNA-seq confirmed abundant expression of beta cell transcription factors and functional markers, including incretin receptors.

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Project description:EndoC-βH1 is emerging as a critical human β cell model to study the genetic and environmental etiologies of β cell (dys)function and diabetes. Comprehensive knowledge of its molecular landscape is lacking, yet required, for effective use of this model. Here, we report chromosomal (spectral karyotyping), genetic (genotyping), epigenomic (ChIP-seq and ATAC-seq), chromatin interaction (Hi-C and Pol2 ChIA-PET), and transcriptomic (RNA-seq and miRNA-seq) maps of EndoC-βH1. Analyses of these maps define known (e.g., PDX1 and ISL1) and putative (e.g., PCSK1 and mir-375) β cell-specific transcriptional cis-regulatory networks and identify allelic effects on cis-regulatory element use. Importantly, comparison with maps generated in primary human islets and/or β cells indicates preservation of chromatin looping but also highlights chromosomal aberrations and fetal genomic signatures in EndoC-βH1. Together, these maps, and a web application we created for their exploration, provide important tools for the design of experiments to probe and manipulate the genetic programs governing β cell identity and (dys)function in diabetes.

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Dexamethasone effect on gene expression in human pancreatic islets and human pancreatic EndoC-βH1 cells

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Project description:We report the 4C (Circularized Chromosome Conformation Capture)-seq data of insulin promoter in EndoC βH1 and HeLa cells.

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