Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genes differentially expressed between NEUROG3-Venus positive and negative hiPSC line differentiated to pancreatic endocrine progenitors [RNA-Seq]

ABSTRACT: Despite this critical role in islet cell development, the precise function and downstream genetic programs regulated directedly by NEUROG3 remain elusive. We therefore mapped genome-wide NEUROG3 occupancy in human induced pluripotent stem cell (iPSC)-derived endocrine progenitors and determined NEUROG3 dependency of associated genes to uncover direct targets. To this aim, we generated a novel hiPSC line (NEUROG3-HA-P2A-Venus), where NEUROG3 is HA-tagged and fused to a self-cleaving fluorescent VENUS reporter. We used the CUT&RUN technique, an alternative method to CHIP-seq allowing transcription factor profiling from a low cell number, to map NEUROG3 occupancy and epigenetic marks in pancreatic endocrine progenitors (PEP) differentiated from this hiPSC line. To optimize the stringency and relevance of NEUROG3 binding sites, we focused our analysis on regions identified both with HA and NEUROG3 antibodies and integrated NEUROG3 occupancy data with chromatin status and gene expression in PEPs and their NEUROG3-dependence. Mapping of NEUROG3 genome occupancy in PEPs uncovers an unexpectedly broad, direct control of the endocrine gene regulatory network (GRN) and raises novel hypotheses on how this master regulator controls islet and beta cell differentiation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE179261 | GEO | 2021/08/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome wide profiling of NEUROG3 occupancy in human pancreatic endocrine progenitors [CUT&RUN]

Project description:Despite this critical role in islet cell development, the precise function and downstream genetic programs regulated directedly by NEUROG3 remain elusive. We therefore mapped genome-wide NEUROG3 occupancy in human induced pluripotent stem cell (iPSC)-derived endocrine progenitors and determined NEUROG3 dependency of associated genes to uncover direct targets. To this aim, we generated a novel hiPSC line (NEUROG3-HA-P2A-Venus), where NEUROG3 is HA-tagged and fused to a self-cleaving fluorescent VENUS reporter. We used the CUT&RUN technique, an alternative method to CHIP-seq allowing transcription factor profiling from a low cell number, to map NEUROG3 occupancy and epigenetic marks in pancreatic endocrine progenitors (PEP) differentiated from this hiPSC line. To optimize the stringency and relevance of NEUROG3 binding sites, we focused our analysis on regions identified both with HA and NEUROG3 antibodies and integrated NEUROG3 occupancy data with chromatin status and gene expression in PEPs and their NEUROG3-dependence. Mapping of NEUROG3 genome occupancy in PEPs uncovers an unexpectedly broad, direct control of the endocrine gene regulatory network (GRN) and raises novel hypotheses on how this master regulator controls islet and beta cell differentiation.

2021-08-04 | GSE171963 | GEO

Open chromatin landscape of pancreatic endocrine progenitors

Project description:During embryonic development, islet progenitors are specified from pancreatic duct cells by transient expression of Neurog3, a transcription factor necessary and sufficient for initiation of islet development. To understand the dynamics of Neurog3-dependent endocrine cell fate determination, in this study we used ATAC-Seq to identify accessible genomic regions of purified duct, endocrine progenitor, and endocrine cells isolated from mice with varying Neurog3 dosage

2020-04-01 | GSE65794 | GEO

Genes differentially expressed between NEUROG3-Venus positive and negative hiPSC line differentiated to pancreatic endocrine progenitors [RNA-Seq]

Project description:Genes differentially expressed between NEUROG3-Venus positive and negative hiPSC line differentiated to pancreatic endocrine progenitors [RNA-Seq]

| PRJNA743030 | ENA

H3K4 trimethylation is required for postnatal pancreatic endocrine cell functional maturation

Project description:During pancreas development, endocrine progenitors differentiate into the islet-cell subtypes, which undergo further functional maturation in postnatal islet development. In islet b-cells, genes involved in glucose-stimulated insulin secretion are activated and glucose exposure increases the insulin response as b-cells mature. Here, we investigated the role of H3K4 trimethylation in endocrine cell differentiation and functional maturation by disrupting TrxG complex histone methyltransferase activity in mouse endocrine progenitors. In the embryo, genetic inactivation of TrxG component Dpy30 in NEUROG3+ cells did not affect the number of endocrine progenitors or endocrine cell differentiation. H3K4 trimethylation was progressively lost in postnatal islets and the mice displayed elevated non-fasting and fasting glycemia, as well as impaired glucose tolerance by postnatal day 24. Although postnatal endocrine cell proportions were equivalent to controls, islet RNA-sequencing revealed a downregulation of genes involved in glucose-stimulated insulin secretion and an upregulation of immature b-cell genes. Comparison of histone modification enrichment profiles in NEUROG3+ endocrine progenitors and mature islets suggested that genes downregulated by loss of H3K4 trimethylation more frequently acquire active histone modifications during maturation. Taken together, these findings suggest that H3K4 trimethylation is required for the activation of genes involved in the functional maturation of pancreatic islet endocrine cells.

2021-05-21 | GSE174751 | GEO

Comparison of Hob6-Venus positive and negative Flk-1+ cells (Venus reporter)

Project description:ES derived Flk-1+ cells were separated by sorting into Hoxb6 positive and negative populations by Venus reporter. Gene expression was compared between these two groups. Duplicate analysis of Hoxb6-Venus positive and negative Flk-1+ cells.

2013-04-16 | E-GEOD-45191 | biostudies-arrayexpress

RNAseq analysis of FACs sorted E-cadherin+, Kit+ and K5-venus+ cells from E15 K5-venus mouse submandibular salivary glands

Project description:We used embryonic day 15 submandibular salivary glands from K5-Venus mice, which were produced using the bovine-K5 promoter driving Venus expression, N=3 separate experiments

2017-01-01 | GSE89896 | GEO

Comparison of Hob6-Venus positive and negative Flk-1+ cells (Venus reporter)

Project description:ES derived Flk-1+ cells were separated by sorting into Hoxb6 positive and negative populations by Venus reporter. Gene expression was compared between these two groups.

2013-04-16 | GSE45191 | GEO

Bulk RNA sequencing of cycling and non-cycling NEUROG3-positive and negative human embryonic stem cell-derived pancreatic cells using a dual NEUROG3-reporter

Project description:Human embryonic stem cells with one allele of the NEUROG3 gene genetically modified into a fusion gene NEUROG3-LINKER-TAGRFPT-P2A-EGFP-NLS were differentiated into the pancreatic lineage until Stage 4 Day 1 of the in vitro differentiation protocol (Rezania et al., 2014, as modified in Petersen et al., 2017). GFP positive and negative cells were FAC-sorted according to their cell cycle state (G0/G1 or G2M), and the global transcriptomes of these four groups were compared using bulk RNA-seq.

2022-12-31 | E-MTAB-11210 | biostudies-arrayexpress

Single-cell RNA sequencing of human embryonic stem cell-derived pancreatic cells enriched for early endocrine progenitors using a novel dual NEUROG3-reporter

Project description:Human embryonic stem cells with one allele of the NEUROG3 gene genetically modified into a fusion gene NEUROG3-LINKER-TAGRFPT-P2A-EGFP-NLS were differentiated into the pancreatic lineage until Stage 4 Day 1 of the in vitro differentiation protocol (Rezania et al., 2014, as modified in Petersen et al., 2017). The cells were index-sorted according to their GFP expression to enrich for low GFP and high GFP cells, and deep single-cell RNA-seq was performed using the plate-based Smart-seq2 platform (Picelli et al. 2014).

2022-12-31 | E-MTAB-11208 | biostudies-arrayexpress

Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network

Project description:Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network

| PRJNA743021 | ENA