Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [ChIP-seq]

ABSTRACT: Developmental defects affecting the pharynx and derived tissues can be found in a variety of syndromes, including DiGeorge, 22q11 deletion, CHARGE and Otofaciocervical syndromes. The associated malformations and dysfunctions of pharynx-derived tissues precipitate phenotypes ranging from malformed features and endocrine disorders to severe immunodeficiency, some of which are associated with high morbidity or elaborate treatment and health care costs. While some of the developmental defects have been linked to mutations or single-nucleotide polymorphisms in transcription factors (TFs) or cis-regulatory elements (CREs), the origin of most pharynx-specific birth defects remain poorly understood and the underlying genetic causes as well as epigenetic context remain elusive. Unfortunately, restricted human tissue access, and discordance of genetic factor requirement and phenotypic penetrance of disease associated human mutations when modeled in mice, has prohibited detailed insights on the molecular basis of mentioned human diseases. Human pluripotent stem cells (hPSCs) could in principle allow for detailed a genetically tractable model to decipher the molecular logic of normal and impaired pharynx development. To unlock hPSC for investigation of pharyngeal malformations and ensuing syndromes, we have developed a differentiation protocol to generate human pharyngeal endoderm in vitro. We have applied multi-omic approaches to characterize the molecular logic of cell fate transitions and developed models of gene regulatory network activities.

ORGANISM(S): Homo sapiens

PROVIDER: GSE222441 | GEO | 2023/08/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [RNA-seq]

Project description:Developmental defects affecting the pharynx and derived tissues can be found in a variety of syndromes, including DiGeorge, 22q11 deletion, CHARGE and Otofaciocervical syndromes. The associated malformations and dysfunctions of pharynx-derived tissues precipitate phenotypes ranging from malformed features and endocrine disorders to severe immunodeficiency, some of which are associated with high morbidity or elaborate treatment and health care costs. While some of the developmental defects have been linked to mutations or single-nucleotide polymorphisms in transcription factors (TFs) or cis-regulatory elements (CREs), the origin of most pharynx-specific birth defects remain poorly understood and the underlying genetic causes as well as epigenetic context remain elusive. Unfortunately, restricted human tissue access, and discordance of genetic factor requirement and phenotypic penetrance of disease associated human mutations when modeled in mice, has prohibited detailed insights on the molecular basis of mentioned human diseases. Human pluripotent stem cells (hPSCs) could in principle allow for detailed a genetically tractable model to decipher the molecular logic of normal and impaired pharynx development. To unlock hPSC for investigation of pharyngeal malformations and ensuing syndromes, we have developed a differentiation protocol to generate human pharyngeal endoderm in vitro. We have applied multi-omic approaches to characterize the molecular logic of cell fate transitions and developed models of gene regulatory network activities.

2023-08-17 | GSE222442 | GEO

Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [ATAC-seq]

2023-08-17 | GSE222439 | GEO

Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [scRNA-Seq]

2023-08-17 | GSE221616 | GEO

Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [scRNA_RA_titration]

2023-08-17 | GSE230563 | GEO

Single-cell genomics profiling of the endoderm of the mouse embryonic pharynx

Project description:Maldevelopment of the pharyngeal endoderm, an embryonic tissue critical for patterning of the pharyngeal region and ensuing organogenesis, ultimately contributes to several classes of human developmental syndromes and disorders. Such syndromes are characterized by a spectrum of phenotypes that currently cannot be fully explained by known mutations or genetic variants due to gaps in characterization of critical drivers of normal and dysfunctional development. Despite the disease-relevance of pharyngeal endoderm, we still lack a comprehensive and integrative view of the molecular basis and gene regulatory networks (GRNs) driving pharyngeal endoderm development. To close this gap, we applied transcriptomic and chromatin accessibility single-cell sequencing technologies to generate a multi-omic developmental resource spanning pharyngeal endoderm patterning to the emergence of organ-specific epithelia in the developing mouse embryo. We identify novel cell-type specific gene regulation, distill GRN models that define developing organ domains, and characterize the role of an immunodeficiency-associated forkhead box transcription factor.

2021-12-20 | GSE182136 | GEO

Single-cell genomics profiling of the endoderm of the mouse embryonic pharynx [scRNA-seq]

2021-12-20 | GSE182135 | GEO

Single-cell genomics profiling of the endoderm of the mouse embryonic pharynx [sc-ATAC-seq]

2021-12-20 | GSE182134 | GEO

Differential gene expression between wild type and Pax9-null pharyngeal arch tissue

Project description:The aim of this study was to identify differentially expressed genes within the pharyngeal arches of Pax9-null embryos at E9.5. Mice null for Pax9 die in the neonatal period with complex cardiovascular defects, caused by abnormal morphogenesis of the pharyngeal arch arteries.

2019-08-28 | GSE128087 | GEO

Benary2021 - tissue dynamics of the hepato-pancreato-biliary organ system

Project description:Single cell-based studies have revealed tremendous cellular heterogeneity in stem cell and progenitor compartments, suggesting continuous differentiation trajectories with intermixing of cells at various states of lineage commitment and notable degree of plasticity during organogenesis. The hepato-pancreato-biliary organ system relies on a small endoderm progenitor compartment that gives rise to a variety of different adult tissues, including liver, pancreas, gallbladder, and extra-hepatic bile ducts. Experimental manipulation of various developmental signals in the mouse embryo underscored important cellular plasticity in this embryonic territory. This is also reflected in the existence of human genetic syndromes as well as congenital or environmentally-caused human malformations featuring multiorgan phenotypes in liver, pancreas and gallbladder. Nevertheless, the precise lineage hierarchy and succession of events leading to the segregation of an endoderm progenitor compartment into hepatic, biliary, and pancreatic structures are not yet established. Here, we combine computational modelling approaches with genetic lineage tracing to assess the tissue dynamics accompanying the ontogeny of the hepato-pancreato-biliary organ system. We show that a multipotent progenitor domain persists at the border between liver and pancreas, even after pancreatic fate is specified, contributing to the formation of several organ derivatives, including the liver. Moreover, using single-cell RNA sequencing we define a specialized niche that possibly supports such extended cell fate plasticity.

2021-07-01 | MODEL2105030001 | BioModels

human nasopharyngeal metagenome

Project description:human nasal/pharyngeal metagenome

| PRJNA338893 | ENA