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Transcriptional profiling of Ngn3-dependent pancreatic endocrine differentiation at E15.5

ABSTRACT: Transcriptional profiling of Ngn3-dependent pancreatic endocrine differentiation at E15.5

PROVIDER: PRJEB8694 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR771141.fastq.gz	Fastqsanger.gz
	ERR771142.fastq.gz	Fastqsanger.gz
	ERR771143.fastq.gz	Fastqsanger.gz
	ERR771144.fastq.gz	Fastqsanger.gz
	ERR771145.fastq.gz	Fastqsanger.gz

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Transcriptional profiling of Ngn3-dependent pancreatic endocrine differentiation at E15.5

Project description:This experiment used RNA-Seq technology to explore gene expression in mouse Ngn3^GFP/+ [het] FACS sorted pancreatic cells at E15.5 (commited endocrine progenitor cells) and in Ngn3^GFP/GFP [null] at E15.5 (defective endocrine progenitor cells). This experiment is designed to understand the gene expression alteration in the endocrine lineage at different embryonic days. The aim is to understand both Ngn3 dependent and independent gene expression profiles so as to reveal the instructive signals that specfy the collective endocrine islet cell fate or specific islet cell type.

2015-10-01 | E-MTAB-3352 | biostudies-arrayexpress

Transcription profiling of mouse Ngn3 expressing cells and endocrine pancreatic cells from wild type and Ngn3 mutant animals at day 15 of embryonic development

Project description:The basic helix-loop-helix transcription factor Neurogenin3 (Ngn3/Neurog3) is expressed in endocrine progenitor cells in the embryonic mouse pancreas. Ngn3 controls endocrine cell fate decisions. Ngn3 deficient mice do not develop any pancreatic endocrine cells, including insulin producing beta cells, and die postnatally from diabetes. Therefore, the characterization of gene expression in Ngn3-expressing cells and their progeny is of particular interest for the development of novel strategies for cell replacement therapies in type-1 diabetes. Here we describe two studies. In the first study (8 assays) we used mice where the EYFP (Enhanced Yellow fluorescent Protein) is expressed under the control of Ngn3 regulatory elements (knock add on strategy). EYFP-positive, Ngn3-expressing cells, were FACS sorted from embryonic pancreas at day 15.5 (E15.5), as well as EYFP-negative cells. In the second study (6 assays) we compared wild-type and Ngn3 mutant pancreas at E15.5. All samples were hybridized to Affymetrix GeneChip Mouse Genome 430.2.0 array.

2009-12-03 | E-CBIL-48 | biostudies-arrayexpress

E-MTAB-3352

Project description:Transcriptional profiling of Ngn3-dependent pancreatic endocrine differentiation at E15.5

2019-05-14 | E-MTAB-3352 | ExpressionAtlas

NGN3 oscillatory expression controls the timing of human pancreatic endocrine differentiation

Project description:Understanding protein expression dynamics is crucial for the mechanistic understanding of cell differentiation. We investigate the dynamics and decoding of NGN3, a transcription factor critical for pancreatic endocrine development. A knock-in endogenous reporter shows that NGN3 protein oscillates with a 13-hour periodicity in human iPS-derived endocrine progenitors and is switched off as cells differentiate to β-like and pre-alpha cells. Increasing NGN3 protein stability results in one broad peak of expression instead of oscillations, with a larger peak to trough fold-change. This leads to precocious endocrine differentiation and earlier expression of key NGN3 target genes. Single-cell analysis of dynamics, mathematical modelling and experimental validation suggest that NGN3 oscillations are decoded by fold-change detection (FCD) rather than the level of expression via an incoherent feedforward loop motif (IFFL) that explains both normal and precocious differentiation. Our findings suggest that oscillatory NGN3 dynamics control the timing of differentiation, but not fate specification.

2025-03-31 | GSE281587 | GEO

The expression order determines the pioneer functions of Ngn3 and NeuroD1 in pancreatic endocrine differentiation

Project description:This study investigates the roles of Ngn3 and NeuroD1 in pancreatic endocrine differentiation. Using a new mouse model, we mapped NGN3 binding sites by CUT&RUN and demonstrated its pioneering role in making chromatin accessible by scATAC-seq. According to conditional knock-out and over-expression experiments and scRNA-seq, we domonstrated that NGN3's pioneering function was dose tolerance, with low doses sufficing, while NeuroD1, as a conventional TF, has no significant pioneer effects under normal phenomena. But when NGN3 was absent, NeuroD1 can alternatively acted as a pioneer factor, and sequential expression of NeuroD1 ahead of Ngn3 predominantly drives α-cell generation.

2025-02-15 | GSE270915 | GEO

Transcriptional Profiling of Ngn3-dependent endocrine progenitors and pre-beta cells

Project description:The goal of this study was to examine genetic networks that control endocrine cell type specification and differentiation. RNA-Seq technology was used to explore the gene expression profiles of pancreatic endocrine progenitor cells (at E10.5 and E15.5), impaired endocrine progenitor cells (at E10.5 and E15.5), and pre-beta cells (at E15.5) in mouse.

2015-01-26 | E-MTAB-3272 | biostudies-arrayexpress

RNA-seq of sorted pancreatic endocrine progenitor cells

Project description:Pancreatic endocrine cells arise from a NGN3+ population during pancreas organogenesis. To gain a more thorough understanding of this progenitor pool, we used a reporter mouse - NGN3-EGFP - and sorted EGFP+ cells from e15.5 pancreata of control animals. The data generated from this experiment will allow us to visualize gene expression levels in endocrine progenitors during normal development and can be used to compare against mutant animal gene expression.

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The expression order determines the pioneer functions of Ngn3 and NeuroD1 in pancreatic endocrine differentiation -2

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Transcription profiling of mouse Ngn3-expressing pancreatic cells in a time series through embryonic development and adult islet cells

Project description:Neurogenin3 (Ngn3) is a basic helix-loop-helix transcription factor which is expressed in scattered cells in the embryonic pancreas. Mice deficient for Ngn3 fail to produce any pancreatic endocrine cells and die shortly after birth. Expression of transcription factors critical to pancreatic development (Isl1, NeuroD, Pax4, and Pax6) is missing and endocrine precursors are absent in mutant pancreatic epithelium. This study utilizes mice which were engineered to contain EGFP (Enhanced Green Fluorescent Protein) under the control of the Ngn3 promoter. In this way, cells which express Ngn3 can be FACS sorted and studied throughout embryonic development (E13.5, E14.5, E15.5, E16.5, and E17.5). EGFP positive cells from the embryonic time-points in addition to adult islets (no cells expressing Ngn3) were hybridized to the BCBC PancChip 6.0 expression microarray, thus generating a profile of gene expression during this critical stage of development of the endocrine pancreas.

2007-12-15 | E-CBIL-40 | biostudies-arrayexpress

Multi-site Neurogenin3 phosphorylation controls pancreatic endocrine differentiation: transcriptomic analysis of pancreatic organoids overexpressing wild type and phosphomutant Neurogenin3

Project description:The proneural transcription factor Neurogenin3 (Ngn3) plays a critical role in pancreatic endocrine cell differentiation. While previous studies have focused on Ngn3 gene function, little is known about the regulation of Ngn3 protein. Here we demonstrate that Ngn3 protein undergoes cyclin-dependent kinase (cdk)-mediated phosphorylation on multiple serine-proline sites. Replacing wild-type protein with a phosphomutant form of Ngn3 increases α-cell generation, the earliest endocrine cell type to be formed in developing pancreas. Mechanistically, preventing multi-site phosphorylation enhances Ngn3 stability and DNA binding, and promotes the expression of target genes that drive differentiation. In addition to perturbing embryonic endocrine differentiation, un(der)phosphorylated Ngn3 contributes to maintaining adult β-cell differentiation in the presence of pro-proliferation cue. Here we perform transcriptomic analysis of a low number of pancreatic organoid cells expressing wild type and phosphomutant Ngn3. Analysis of the endocrine differentiation programme activated by Ngn3 in this context revealed the cell fate plasticity of the system and demonstrated that preventing Ngn3 phosphorylation enhances endocrine gene expression.

2017-06-09 | GSE96707 | GEO

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