|
| Status |
Public on Aug 17, 2023 |
| Title |
Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development [RNA-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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.
|
| |
|
| Overall design |
Gene expression profiling analysis of RNA-seq data from a directed differentiation protocol of human embryonic stem cells (hESCs) toward pharyngeal foregut endoderm (hPFE). 4 timepoints are profiled : hESC, definitive endoderm (hDE), anterior foregut endoderm (hAFE) and hPFE with 2 replicates each
|
| |
|
| Contributor(s) |
Kearns NA, Lobo M, Genga RM, Abramowitz RG, Parsi M, Min J, Kernfeld EM, Huey JD, Kady J, Brehm MA, Ziller MJ, Maehr R |
| Citation(s) |
37751684 |
| |
| Submission date |
Jan 09, 2023 |
| Last update date |
Nov 20, 2023 |
| Contact name |
René Maehr |
| E-mail(s) |
rene.maehr@umassmed.edu
|
| Organization name |
UMass Medical School
|
| Department |
Program in Molecular Medicine/Diabetes Center of Excellence
|
| Lab |
Maehr Lab
|
| Street address |
368 Plantation St
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (8)
|
|
| This SubSeries is part of SuperSeries: |
| GSE222443 |
Using human pluripotent stem cells to dissect the molecular basis of human pharyngeal endoderm development II |
|
| Relations |
| BioProject |
PRJNA922113 |
| SRA |
SRP416611 |
Less...
More...