Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A comprehensive characterisation of fetal and mature retinal cell identity to assess the fidelity of retinal organoids

ABSTRACT: Retinal organoids derived from pluripotent stem cells have been widely used to model development and disease of the human eye. Yet there is a lack of studies that have systematically evaluated the fidelity of the organoids to their in vivo counterpart. This is particularly relevant for evaluating the efficacy of therapeutic applications and culture protocol performance. To this end, we performed an extensive meta-atlas characterisation of cellular identities of the human eye, covering a wide range of developmental stages. The resulting map uncovered previously unknown biomarkers of major retinal cell types and those associated with cell-type specific maturation. Using these retinal identities from fetal and adult tissue as the map, we systematically assessed the fidelity of the retinal organoids to mimic the human eye, enabling us to comprehensively benchmark the current protocols for retinal organoid generation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE201356 | GEO | 2022/12/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A comprehensive characterisation of fetal and mature retinal cell identity to assess the fidelity of retinal organoids

Project description:A comprehensive characterisation of fetal and mature retinal cell identity to assess the fidelity of retinal organoids

| PRJNA830973 | ENA

Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids

Project description:This SuperSeries is composed of the SubSeries listed below. We have generated high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive and developmental stage-specific alterations in DNA topology and correlate these changes with transcription of cell type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift towards A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages of TADs (i.e., TAD cliques) tend to localize in the active chromatin regions with binding sites for eye-field transcription factors. These genes show a gain of chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits.

2023-11-03 | GSE229683 | GEO

Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids

Project description:We have generated high-resolution Hi-C map of developing human retinal organoids to elucidate spatiotemporal dynamics of genomic architecture and its relationship with gene expression patterns. We demonstrate progressive and developmental stage-specific alterations in DNA topology and correlate these changes with transcription of cell type-restricted gene markers during retinal differentiation. Temporal Hi-C reveals a shift towards A compartment for protein-coding genes and B compartment for non-coding RNAs, displaying high and low expression respectively. Notably, retina-enriched genes are clustered near lost boundaries of topologically associated domains (TADs), and higher-order assemblages of TADs (i.e., TAD cliques) tend to localize in the active chromatin regions with binding sites for eye-field transcription factors. These genes show a gain of chromatin contacts at their transcription start site as organoid differentiation proceeds. Our study provides a global view of chromatin architecture dynamics associated with diversification of cell types during retinal development and serves as a foundational resource for in-depth functional investigations of retinal developmental traits.

2023-11-03 | GSE229682 | GEO

Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids

2023-11-03 | GSE229681 | GEO

Transcription profiling of human and mouse first passage vs. primary retinal sphere cells

Project description:The pigmented portion of ciliary epithelium in the adult mammalian eye harbors mitotically quiescent retinal sphere cells, which are capable of self-renewal and differentiating into retinal neurons when assayed in vitro; however, very little is known about the molecular mechanism controlling the proliferation and differentiation of these adult retinal stem cells or their molecular resemblance to mutipotent stem/progenitor cells during early eye development. This experiment studies the gene expression of first passage and primary human and mouse retinal sphere cells. Experiment Overall Design: this experiment include 4 samples and 12 replicates

2008-06-12 | E-GEOD-3791 | biostudies-arrayexpress

Transcriptomic features of hiPSC-derived cells with a good capability to generate retinal organoids

Project description:Purpose: To identify transcriptomic features of hiPSC-derived cells with a good capability to generate retinal organoids Methods: Human induced pluripotent stem cell (hiPSC) samples were collected at two time points for RNA sequencing (day zero and seven, each time point in triplicate). Cell pellets were collected and flash frozen. Total RNA was extracted by a phenol/chloroform method using TRIzol LS reagent (ThermoFisher Scientific, MA) according to the manufacturer's guidelines. tRNA was treated with DNAse I prior to library preparations being performed for RNAsequencing. Results: Human iPSC lines show variation in their ability to differentiate into a neuroectodermal/early eye field phenotype. This study identified a panel of signature transcripts that were differentially expressed at seven days of differentiation, between lines of low- and high-retinal propensity. Conclusions: This study provides a gene profile that identifies which hiPSC-derived cells have a good capability to generate retinal organoids. This allows for the analysis of retinal propensity by quantitative PCR within the first seven days of differentiation.

2023-06-21 | GSE192665 | GEO

Single cell transcriptomic comparison of human fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures.

Project description:To study the development of human retina, we used single cell RNAseq at key fetal stages and followed the development of the major cell types, as well as populations of transitional cells. We also analyzed stem cell (hPSC)-derived retinal organoids; although organoids have a very similar cellular composition at equivalent ages to the fetal retina, there are some differences in gene expression of particular cell types. Moreover, the inner retinal lamination is disrupted in more advanced stages of organoids when compared with fetal retina. To determine whether the disorganization in the inner retina was due to the culture conditions, we analyzed retinal development in fetal retina maintained under similar conditions. These retinospheres develop for at least 6 months, displaying better inner retinal lamination than retinal organoids. Our scRNAseq comparisons between fetal retina, retinal organoids and retinospheres provide a new resource for developing better in vitro models for retinal disease.

2020-01-10 | GSE142526 | GEO

Transcriptomics of CD29+/CD44+ cells isolated from hPSC retinal organoids reveals a cell population with retinal progenitor and Müller glia characteristics.

Project description:Müller glia play very important and diverse roles in retinal homeostasis and disease, bur very little is known of their development during human retinal embryogenesis. Since they share several markers with retinal progenitors, they are often considered as a different cell population. In this study we isolated CD29+/CD44+cells from retinal organoids formed by hEPSC cells in vitro, and examined their transcriptome profile at various stages of organoid development to identify their transcriptomic profile.

2023-02-21 | E-MTAB-12467 | biostudies-arrayexpress

Mosaic perturbation of transcription factors in human retinal organoid development

Project description:To begin to understand how TFs regulate retinal cell type identity in human tissues, we established a pooled loss of function (LOF) experiment based on the CROP-seq protocol in developed retinal organoids. We targeted five TFs (OTX2, NRL, CRX, VSX2, and PAX6) that are important for retinal development and expressed dynamically over the organoid developmental time course.

2023-02-24 | E-MTAB-12622 | biostudies-arrayexpress

Deciphering the spatio-temporal transcriptional and chromatin accessibility of human retinal organoid development at the single cell level [scRNA-Seq]

Project description:Molecular information on the very early stages of human retinal development remains scarce due to limitations in obtaining human eye samples of less than six weeks old. Pluripotent stem cell derived retinal organoids provide an unprecedented opportunity for studying human retinal development; however their ability to fully recapitulate early retinal development has not been assessed as yet. Using a combination of scRNA-Seq and ST approaches, we present for the first time a genome wide, single cell spatio-temporal transcriptome of retinal organoid development. Our data demonstrate that retinal organoids recapitulate key events of retinogenesis including optic vesicle/cup formation, formation of a putative ciliary margin zone, emergence of RPCs and their precise and orderly differentiation to various types of retinal neurons. Combining the scRNA- with scATAC-Seq data, we were able to reveal cell type specific transcription factor binding motifs on accessible chromatin at each stage of organoid development and to show that chromatin accessibility is highly correlated to the developing human retina, but with some differences in the temporal emergence and abundance of some of the retinal cell types. Our work provides the first integrated molecular and spatial atlas of human retinal organoid development that could be used to identify novel genes and key pathways that underpin human retinal development and function.

2024-02-15 | GSE235582 | GEO

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