Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity

ABSTRACT: Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity

PROVIDER: PRJNA910936 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22676500.fastq.gz	Fastqsanger.gz
	SRR22676501.fastq.gz	Fastqsanger.gz
	SRR22676502.fastq.gz	Fastqsanger.gz
	SRR22676503.fastq.gz	Fastqsanger.gz
	SRR22676504.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 105

Similar Datasets

Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity

Project description:With a critical need for more complete in vitro models of human development and disease, organoids hold immense potential. Their complex cellular composition makes single-cell sequencing of great utility; however, the limitation of current technologies to a handful of treatment conditions restricts their use in screens or studies of organoid heterogeneity. Here, we apply sci-Plex, a single-cell combinatorial indexing (sci)-based RNA-seq multiplexing method to retinal organoids. We demonstrate that sci-Plex and 10x methods produce highly concordant cell type compositions and then expand sci-Plex to analyze the cell type composition of 410 organoids upon modulation of critical developmental pathways. Leveraging individual organoid data, we develop a method to measure organoid heterogeneity, and we identify that activation of Wnt signaling early in retinal organoid cultures increases retinal cell types up to six weeks later. Our data show sci-Plex’s potential to dramatically scale-up the analysis of treatment conditions on relevant human models.

2022-12-14 | GSE220661 | GEO

Single-cell sequencing of individual retinal organoids reveals determinants of cell fate heterogeneity.

Project description: Not available

| S-EPMC10312535 | biostudies-literature

Single-cell sequencing of individual retinal organoids reveals determinants of cell-fate heterogeneity.

Project description: Not available

| S-EPMC10475847 | biostudies-literature

FOXM1 dependent regulation of retinal pigment epithelium cell fate

Project description:FOXM1 dependent regulation of retinal pigment epithelium cell fate

| PRJEB7893 | ENA

Retinoic acid drives cell fate specification, maturation and retinal regionality in human retinal organoids [Visium]

Project description:Retinoic acid (RA) is a key morphogen in human retinal development, activating transcriptional programs that drive retinal progenitor differentiation and photoreceptor development, ensuring proper spatial organisation within the neural retina, essential for vision. Despite its well-established role in retinal patterning, the concentration-dependent effects of RA on human retinal cell fate specification and the regional definition of the primate macula and peripheral retina remain poorly understood. Here, we show that temporal and dosage-dependant modulation of RA during human retinal organoid differentiation induces distinct changes in retinal cell abundance, maturation, and organisation. Single-cell transcriptomics and protein analysis revealed that RA dosage influenced the relative abundance and maturation of photoreceptors and retinal interneurons. Spatial transcriptomics analyses demonstrated that low RA levels biased retinal organoids toward a macular-like regional identity, whereas high RA levels promoted peripheral-like development. Collectively, our findings emphasise the critical role of RA signalling in retinal maturation and regional specification. This study elucidates mechanisms involved in human retinal development and we anticipate that controlled RA modulation in retinal organoids provides a strategy to refine disease modelling of inherited retinal disorders and enhance the specific generation of photoreceptors suitable for transplantation and regenerative therapies.

2026-03-22 | GSE293582 | GEO

FOXM1 dependent regulation of retinal pigment epithelium cell fate

Project description:The integrity of the epithelium is maintained by a complex but regulated interplay of processes that allow seamless orchestration of a proliferative state into a stably differentiated state. In this study, using stem cell derived Retinal Pigment Epithelium (RPE) cells as a model; we have investigated the molecular mechanisms that affect attainment of the epithelial phenotype. We identify a novel role for the proto-oncogene FOXM1 in determining epithelial fate of RPE by directly regulating cell proliferation and by indirectly regulating expression of signalling factors BMP7 and Wnt5B; both of which are intimately required for eventual acquisition of the epithelial phenotype. This study uncovers the role of FOXM1 in a non-oncogenic, native-like setting and shows that human ES derived RPE can serve as a useful model system to address biological questions not restricted to visual function.

2015-07-24 | E-MTAB-3137 | biostudies-arrayexpress

Retinoic acid drives cell fate specification, maturation and retinal regionality in human retinal organoids [Stereo-seq]

2026-03-22 | GSE293464 | GEO

Retinoic acid drives cell fate specification, maturation and retinal regionality in human retinal organoids [scRNA-seq]

2026-03-22 | GSE293457 | GEO

Retinoic acid drives cell fate specification, maturation and retinal regionality in human retinal organoids [Visium]

Project description:Retinoic acid drives cell fate specification, maturation and retinal regionality in human retinal organoids [Visium]

| PRJNA1245288 | ENA

Yap and Taz regulate retinal pigment epithelial cell fate

Project description:The optic vesicle comprises a pool of bi-potential progenitor cells from which the retinal pigment epithelium (RPE) and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation, but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz-Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises, and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap (yap1) mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz (wwtr1) mutant alleles such that, when Yap and Taz are both absent, optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co-factor. In contrast to loss of Yap and Taz, overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall, this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.

2015-08-06 | E-GEOD-71681 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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