Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional dynamics of iPSC differentiation into β cells revealed by single-cell RNA sequencing

ABSTRACT: Induced pluripotent stem cells can be differentiated in vitro into insulin-producing β cells. In this study we unveil the transcriptional dynamics of the differentiation and explain the heterogeneity of the final cell product, in comparison with β cells from organ donors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE149613 | GEO | 2020/10/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptional dynamics of iPSC differentiation into β cells revealed by single-cell RNA sequencing

Project description:Transcriptional dynamics of iPSC differentiation into β cells revealed by single-cell RNA sequencing

| PRJNA629364 | ENA

Proteomic profiling of human iPSC-derived pancreatic endocrine cells for the identification of clinical biomarkers

Project description:Great progresses have been made for generating in vitro pluripotent stem cell pancreatic β-like cells. However, the maturation stage of the cells still requires in vivo maturation to recreate the environmental niche. A deeper understanding of the factors promoting maturation of the cells is of great interest for clinical applications. We performed label-free mass spectrometry-based proteomic analysis of samples from a longitudinal study of differentiation of human-induced pluripotent stem cells towards glucose-responsive insulin producing cells.

2018-04-04 | PXD008267 | Pride

Stabilized biological production by product addiction

Project description:Populations of engineered metabolite-producing microorganisms are prone to evolutionary production declines during industrial-scale cultivations. In this study, we develop a synthetic product addiction system in E coli that addicts mevalonic acid production cells to mevalonic acid. Through experimentally simuluated long-term fermentation, we investigate how product-addicted organisms remain stable and avoid formation of genetic subpopulations of fit, non-producing cells.

2018-02-09 | E-MTAB-6182 | biostudies-arrayexpress

A SRp55-regulated alternative splicing network controls pancreatic beta cell survival and function

Project description:Progressive failure of insulin-producing beta cells is the central event leading to diabetes, yet the signalling networks controlling beta cell fate remain poorly understood. Here we show that SRp55, a splicing factor regulated by the diabetes susceptibility gene GLIS3, has a major role in maintaining function and survival of human beta cells. RNA-seq analysis revealed that SRp55 regulates the splicing of genes involved in cell survival and death, insulin secretion and JNK signalling. Specifically, SRp55-mediated splicing changes modulate the function of the pro-apoptotic proteins BIM and BAX, JNK signalling and endoplasmic reticulum stress, explaining why SRp55 depletion triggers beta cell apoptosis. Furthermore, SRp55 depletion inhibits beta cell mitochondrial function, explaining the observed decrease in insulin release. These data unveil a novel layer of regulation of human beta cell function and survival, namely alternative splicing modulated by key splicing regulators such as SRp55 that may crosstalk with candidate genes for diabetes.

2018-02-02 | GSE98485 | GEO

Transcriptomic analysis revealed the mechanisms involved in the differential accumulation of taxoids, flavonoids and hormones among three Taxaceae trees

Project description:The natural product taxol is an efficient and worldwide accepted anticancer drug. Taxol and other taxoids accumulate in only a few specific genera of the Taxaceae family, such as Taxus and Pseudotaxus. The comprehensive variations among three Taxaceae trees, including one taxol-producing (TP) and two non-taxol producing (NTP) trees, were compared. In total, 3,655 metabolites and 88,609 functional genes were identified through metabolomic and transcriptomic analyses, respectively. KEGG enrichment analysis showed that many differentially expressed genes were enriched in several hormone-, flavonoid-, and terpenoid-related metabolic pathways. The hormones, abscisate and abscisic acid, highly accumulated in the NTP trees, whereas gibberellic acids substantially accumulated in the TP trees.

2018-10-27 | GSE121831 | GEO

Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β-cells [iPSC scRNAseq]

Project description:IFNa is a key regulator of the dialogue between pancreatic β-cells and the immune system in early type 1 diabetes (T1D). IFNa up-regulates HLA class I expression in human β-cells fostering autoantigen presentation to the immune system. We observed by bulk and single cell RNA sequencing that exposure of human induced pluripotent-derived islet-like cells to IFNa induces expression of HLA class I and of other genes involved in antigen presentation, including the transcriptional activator NLRC5. We next evaluated the global role of NLRC5 in human insulin-producing EndoC-βH1 and human islets cells by RNA sequencing and targeted gene/protein determination. NLRC5 regulates expression of HLA class I expression and related genes and of chemokines. NLRC5 also mediates the effects of IFNa on alternative splicing, a generator of β-cell neoantigens, suggesting that it is a central mediator of the effects of IFNa on β-cells that contribute to trigger and amplify autoimmunity in T1D.

2022-09-14 | GSE203384 | GEO

Project description:Metagenomic analysis of raw material and final product samples from dairy facilities

| PRJNA997801 | ENA

Conventional and neo-antigenic peptides naturally processed and presented by beta cells are targeted by circulating naïve CD8+ T cells in type 1 diabetic and healthy donors

Project description:Human CD8+ T cells are the final mediators of autoimmune β-cell destruction in type 1 diabetes. However, their target epitopes have not been demonstrated to be naturally processed and presented by β cells. We therefore performed an epitope discovery study combining HLA Class I peptidomics and transcriptomics strategies. Inflammatory cytokines increased β-cell peptide presentation in vitro, paralleling upregulation of HLA Class I expression. Peptide sources included known β-cell antigens and several insulin granule proteins. Preproinsulin yielded multiple previously described HLA-A2-restricted epitopes. Secretogranin V (SCG5/7B2), proconvertase-2, urocortin-3 and the insulin gene enhancer protein ISL-1 were identified as novel β-cell antigens, which were processed into HLA-A2-restricted epitopes recognized by circulating naïve CD8+ T cells in type 1 diabetic and healthy donors. HLA-A2-bound neo-epitopes were also represented and originated from an alternative mRNA splice isoform (SCG5-009) and from an islet amyloid polypeptide transpeptidation product. This first description of the β-cell HLA peptidome opens new avenues to understand the antigen processing pathways employed by β cells and provides a valuable tool for developing T-cell biomarkers and tolerogenic vaccination strategies.

2018-08-02 | GSE108413 | GEO

microRNAseq of primary human gallbladder cells, reprogrammed human gallbladder cells, and human pancreatic beta cells

Project description:We determined the global microRNA expression profiles of primary human gallbladder cells and genetically reprogrammed human gallbladder cells and compared with pancreatic beta cells to ascertain the degree of cellular transdifferentatiation of insulin-producing human gallbladder cells to become beta-like cells. First, we cultured patient-derived gallbladder cells and then we transduced these with beta cell transcription factors to reprogram gallbladder cells to become beta-like cells. We used a pan-islet surface monoclonal antibody to enrich for insulin-producing reprogrammed human gallbladder cells using FACS.

2017-08-02 | E-MTAB-5554 | biostudies-arrayexpress

RNAseq of primary human gallbladder cells, reprogrammed human gallbladder cells, and human pancreatic beta cells

Project description:We determined the global gene expression profiles of primary human gallbladder cells and genetically reprogrammed human gallbladder cells and compared with pancreatic beta cells to ascertain the degree of cellular transdifferentatiation of insulin-producing human gallbladder cells to become beta-like cells. First, we cultured patient-derived gallbladder cells and then we transduced these with beta cell transcription factors to reprogram gallbladder cells to become beta-like cells. We used a pan-islet surface monoclonal antibody to enrich for insulin-producing reprogrammed human gallbladder cells using FACS.

2017-08-02 | E-MTAB-5556 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data