Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A SIX6 reporter for studies of early optic development

ABSTRACT: Human pluripotent stem cells represent an exciting tool to investigate the mechanisms of human eye development and to build human models of retinal dystrophy. To explore the dynamics of early eye development in a carefully controlled setting and optimize this process, we have developed an eyefield expressed SIX6-GFP reporter that enables the systematic optimization of early eye-field development allowing the identification of conditions that favor early optic development.

ORGANISM(S): Homo sapiens

PROVIDER: GSE179260 | GEO | 2021/08/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

SIX6 regulation in human optic vesicles is mediated by early microenvironmenta factors

Project description:Human pluripotent stem cells (PSCs) represent an exciting tool to investigate the mechanisms of human eye development and to build models of human retinal disease. When grown in 3D, these cells can self-organize into laminar organized retinas; however, significant variation in the size, shape and composition of individual organoids exists, and this variation can create challenges. Neither the microenvironment nor the timing of critical growth factors driving eye formation or retinogenesis are fully understood. To explore the dynamics of early retinal organoid development, we have developed a SIX6-GFP reporter line that enables the systematic optimization of early eye field development, allowing for the identification of conditions that favor optic development. We found that SIX6 expression in 3D optic structures is influenced by small molecules regulating SHH and WNT signaling in a dose and time dependent fashion. In addition, we demonstrated that hypoxic growth conditions favor SIX6 expression, and promote eye formation. The systematic optimization of these pathways leads to optic vesicles with robust SIX6 expression and global gene expression profiles consistent with a retinal identity. The use of stem cell derived human retinal organoids with a real time marker for retinogenesis, therefore, represents an important model for probing the mechanisms of early human eye development.

2021-10-25 | GSE148168 | GEO

A SIX6 reporter for studies of early optic development

Project description:A SIX6 reporter for studies of early optic development

| PRJNA743024 | ENA

SIX6 regulation in human optic vesicles is mediated by early microenvironmenta factors

Project description:SIX6 regulation in human optic vesicles is mediated by early microenvironmenta factors

| PRJNA623366 | ENA

Danio rerio

Project description:Zebrafish early eye development

| PRJNA120923 | ENA

Zfp503/Nlz2 is Required for RPE Differentiation and Optic Fissure Closure

Project description:Uveal coloboma is a congenital eye malformation caused by failure of the optic fissure to close in early human development. Despite significant progress in identifying genes whose regulation is important for executing this closure, mutations are detected in a minority of cases using known gene panels, implying additional genetic complexity. We show that the mouse Zfp503/Nlz2 gene is dynamically regulated in developing mouse eyes and that loss of its expression results in uveal coloboma. KO embryos exhibit altered expression patterns of several key transcription factors involved in eye development, including Otx2, Mitf, Pax6, Pax2, Vax1 and Vax2, resulting in reduced melanin pigmentation in the presumptive retinal pigment epithelium and its differentiation into a neural-retina-like lineage. From a large cohort of patients with exome sequencing records, only one patient with clinical diagnosis of retinal degeneration was identified carrying a pPresumed loss-of-function variants in the human ortholog, ZNF503. Although no disease-causing association was demonstrated, because of the retinal degeneration rather than of uveal coloboma phenotype, are rare and may be associated with retinal degeneration, rather than a uveal coloboma phenotype, suggesting it is tempting to speculate that a pleiotropic role of ZNF503 might have a pleiotropic role in ocular development and physiology

2022-11-16 | GSE180641 | GEO

Wnt ligands from the embryonic surface ectoderm regulate bimetallic strip optic cup morphogenesis in the mouse

Project description:Wnt signaling in early eye development, specifically the lens placode shows expression of 12 out of 19 Wnt ligands. We these Wnt activities were suppressed using conditional deletion of Wntless, dramatic phenotypic changes in morphogensis occurred. Microarray analysis of the genes that were changed in response to deletion of Wnt ligands in the developing eye region show direct or indirect responses from the surface ectoderm to the developing RPE and optic cup curvature, creating an overal shape change phenotype in the bilayerd epithelium of the optic cup. Mouse embryos at embryonic stage e10.5 were disected into pbs and eye regions were disected and removed for RNA extraction and hybridization to Affymetrix microarrays. We sought to identify the genes that were changed in response to deletion of Wls from the developing surface ectoderm of the eye region. Genes changed could be the direct or indirect result from deleltion of Wls from the surface ectoderm using the LeCre recombinase gene as a tool for analysis.

2015-01-22 | E-GEOD-65154 | biostudies-arrayexpress

Wnt ligands from the embryonic surface ectoderm regulate bimetallic strip optic cup morphogenesis in the mouse

2015-01-22 | GSE65154 | GEO

Expression data from mouse optic nerve head after optic nerve crush

Project description:Reactive gliosis is a complex process that involves profound changes in gene expression. We used microarray to indentify differentially expressed genes and to investigate the molecular mechanisms of reactive gliosis in optic nerve head in response to optic nerve crush injury. C57Bl/6 female mice were 6-8 weeks old at the time of optic nerve crush surgery. The optic nerve in the left eye was crush 1 mm behind the globe for 10 seconds and the right eye served as contralateral control. The animals were allowed to recover for 1 day, 3 day, 1 week, 3 weeks and 3 months before the optic nerve heads were collected. The naive control mice did not receive any surgery in either eye. Due to the small tissue size of the mouse optic nerve head, two optic nerve heads were pooled together for each microarray chip. The left eyes and the right eyes of two mice were combined respectively to form one pair of experiment and control samples. There were five biological replicates (10 mice) for each condition.

2013-07-15 | E-GEOD-40857 | biostudies-arrayexpress

High-throughput reporter assay for human genetic variants overlapping ATF4 binding sites

Project description:Activating Transcription Factor 4 (ATF4) is a transcription factor that regulates cellular responses to nutrient deficiency, endoplasmic reticulum stress and oxidative stress. At the organism level, it is implicated in processes such as hematopoiesis, skeletogenesis, eye development, memory, muscle atrophy, and carbohydrate and lipid metabolism. Here, we carried out a massively parallel reporter assay (MPRA) to identify allelic regulatory effects of human genetic variants that reside in ATF4 binding sites identified in ChIP-Seq experiments.

2023-12-01 | GSE225216 | GEO

Transcription profiling of mouse embryo eye development, specifically optic fissure.

Project description:The different stages of the optic fissure can be clearly visualized by making sagittal sections through the mouse eye during early development which represent the optic fissure at open (E10.5), closing (E11.5) and fused (E12.5) states. Laser capture microdissection (LCM) was employed to dissect tissue from the margins of the optic fissure consisting of the outer (presumptive RPE) and inner (presumptive neurosensory retina) layers of the retina. An approximately square-shaped block of optic fissure (50 x 50 mm) was dissected from each side of the fissure. Two rounds of linear amplification were performed on RNA isolated from each of the samples prior to microarray hybridization. Expression data were gathered in biological triplicate at E10.5, E11.5 and duplicate at E12.5, each array representing pooled optic fissure tissue from three embryos from a single litter. Expression signals were ascertained from 45,101 probe sets and normalized across arrays. Experiment Overall Design: Differential gene expression over the course of three days in laser capture microdissected tissue from wild type mouse embryos.

2008-10-26 | E-GEOD-13103 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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