Single-Cell RNA Sequencing of Retinal Organoids Drived from CSC14 hESCs
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PROVIDER: PRJEB48323 | ENA |
REPOSITORIES: ENA
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Project description:Retinal organoids samples that derived from human embryonic stem cells were analyzed by single-cell RNA sequencing. Two samples at different differentiation stages (day57 and day 171) were included in this study for cell type comparison.
2022-01-01 | E-MTAB-11121 | biostudies-arrayexpress
Project description:Single-Cell RNA Sequencing of Retinal Organoids Derived by CSC14 hESCs
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2023-03-27 | E-MTAB-11990 | biostudies-arrayexpress
Project description:hESC lines carrying deleterious mutations in the RB1 gene in heterozygous and homozygous state were generated by genome-editing based on CRISPR/Cas9. Parental cell line and genome-edited cell lines were differentiated into retinal organoids for 152 days based on the Protocol published by Döpper et al., Current protocols, PMID: 32956559. Briefly, single cells were reaggregated in presence of dual SMAD and WNT-inhibition; retinal tissue became visible from day 12 onward. BMP4-induction and addition of small molecules CHIR99021 and SU5402 directed differentiation towards retina and retinal pigment epithelium. Long-term differentiation was carried out in the presence of 10% FBS, taurine and retinoic acids. Organoids were collected at indicated time points and either embedded for cryosectioning and immunostaining or frozen at -80°C for RNA preparation.
2022-05-10 | E-MTAB-10331 | biostudies-arrayexpress
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
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
Project description:The macula of the retina has a high ratio of cones to rods and is critical for central vision and visual acuity. Here we report the generation, transcriptome profiling, and functional validation of single cells from cone-enriched human retinal organoids differentiated from hESCs. Single-cell RNA-seq of 8-month retinal organoids identified clusters of cone and rod photoreceptors and confirmed the cone enrichment initially revealed by immunostaining. Collectively, we have established cone-enriched retinal organoids and a reference of transcriptomes that are rich resources for retinal studies.
2019-04-25 | GSE119343 | GEO
Project description:Single cell genomic analyses provide a new perspective on the development of complex tissues, like the vertebrate neural retina. We previously used single cell transcriptomic analysis to characterize human fetal retinal development and assessed the degree to which retinal organoids recapitulate normal fetal development. In this study we extend the transcriptomic analyses of fetal human retina to incorporate single nuclear scATAC-seq, a powerful new method to characterize potential gene regulatory networks through the changes in accessible chromatin that accompany cell state changes. The combination of scATAC-seq and sc-RNA-seq can be used to study the process of neurogenesis in the developing fetal human retina at unprecedented resolution. We identify the key transcription factors relevant to specific fates and the order of the transcription factor cascades that define each of the major retinal cell types. These transcriptomic and epigenomic features are largely recapitulated in retinal organoids; however, there are differences in Notch signaling and amacrine cell gene regulation, which are not as robust in organoids. The datasets we generated constitute an excellent resource for the continued improvement of retinal organoid technology, and have the potential to inform and accelerate regenerative medicine approaches to retinal disease.
2021-12-30 | GSE184386 | GEO
Project description:The macula of the retina has a high ratio of cones to rods and is critical for central vision and visual acuity. Macula degenerations affect vision the most and are incurable. Here we report the generation, transcriptome profiling, and functional validation of cone-enriched human retinal organoids differentiated from hESCs. Transcriptome profiling using bulk RNA-seq demonstrated that retinal differentiation in vitro recapitulated retinogenesis in vivo in the temporal expression of cell differentiation markers and retinal disease genes, as well as in mRNA alternative splicing. Single-cell RNA-seq of 8-month retinal organoids identified clusters of cone and rod photoreceptors and confirmed the cone enrichment initially revealed by immunostaining. Notably, comparisons of single-cell transcriptomes demonstrated the similarity between retinal organoids and human macula in cones and rods. Cones in retinal organoids exhibited electrophysiological functions. Collectively, we have established cone-enriched retinal organoids and a reference of transcriptomes that are rich resources for retinal studies.
2019-04-25 | GSE119274 | GEO
Project description:The rapid improvements in single cell sequencing technologies and analyses methods afford greater scope for dissecting organoid cultures composed of multiple cell types and create an opportunity to interrogate these models to understand tissue biology, cellular behaviour and interactions. To this end, retinal organoids generated from human embryonic stem cells (hESCs) were analysed by single cell RNA-Sequencing at three time points of differentiation. Combinatorial data from all time points revealed the presence of nine clusters, five of which corresponded to key retinal cell types, namely retinal pigment epithelium (RPE), retinal ganglion cells (RGCs), cone and rod photoreceptors and Müller glia cells. The remaining four clusters expressed genes typical of mitotic cells, extracellular matrix (ECM) components and those involved in retinal homeostasis. The cell clustering analysis revealed the decreasing presence of mitotic cells and RGCs, formation of a distinct RPE cluster, the emergence of cone and rod photoreceptors from photoreceptor precursors and an increasing number of Müller Glia cells over time. The pseudotime analysis resembled the order of cell birth during retinal development, with the mitotic cluster commencing the trajectory and the large majority of Müller glia being the latest. Together, these data demonstrate the feasibility and potential of single cell RNA-Seq to dissect the inherent complexity of the organoids and the orderly birth of key retinal cell types.
2018-12-19 | GSE119893 | GEO