Deconstructing Retinal Organoids: single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina
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PROVIDER: PRJNA490648 | ENA |
REPOSITORIES: ENA
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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
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:Single cell RNA sequencing (scRNA-seq) has advanced the assessment of cellular heterogeneity at the single-cell resolution by identifying transcriptional similarities and differences. Data resources of scRNA-seq have been largely produced and extensively studied for the mouse retina. They serve as a powerful tool to study cellular components, transcriptome relationships, and regulatory mechanisms underlying various retinal diseases and biological processes. The large volume of mouse retinal scRNA-seq data has been released in separate repositories, limiting their widespread use in mouse retina communities. In this work, we are presenting a unified single-cell atlas for adult wild-type mouse retina using our in-house generated single-cell RNA-seq data complementing public datasets. The collected data account for over 323,000 single cells. After data integration, cell clustering, and cell type annotation, we have annotated 11 major classes and over 120 retinal cell types to form a unified single-cell reference for the mouse retina. To facilitate the public use of the reference, we have deposited it on CELLxGENE, UCSC Cell Browser, and Single Cell Portal for visualization and gene expression exploration. The unified atlas is also released to annotate new mouse retinal cells using scArches utilities. This unified reference serves an easy-to-use data resource of mouse retina communities.
2024-02-15 | GSE243413 | GEO
Project description: Not available
| S-EPMC6519347 | biostudies-literature
Project description:Purpose: Investigate the molecular determinants of retinal regeneration in adult vertebrates by analyzing the gene expression profiles of control and post-lesion retina of adult zebrafish, a system that regenerates following injury. Methods: Gene expression profiles of zebrafish retina and brain were determined with DNA microarray, RT-PCR, and real-time quantitative PCR analyses. Damaged retinas and their corresponding controls were analyzed 2-5 days post-lesion (acute injury condition) or 14 d post-lesion (cell regeneration condition). Results: Expected similarities and differences in the gene expression profile of zebrafish retina and brain were observed, confirming the applicability of the gene expression techniques. Mechanical lesion of retina triggered significant, time-dependent changes in retinal gene expression. The induced transcriptional changes were consistent with cellular phenomena known to occur, in a time-dependent manner, subsequent to retinal lesion, including cell cycle progression, axonal regeneration, and regenerative cytogenesis. Conclusions: The results indicate that retinal regeneration in adult zebrafish involves a complex set of induced, targeted changes in gene transcription, and suggest that these molecular changes underlie the ability of the adult vertebrate retina to regenerate. Keywords: time course; injury response; cellular correlation Control brain and retina (unlesioned); Control and lesioned retina (matched animals, at least n = 8 for each condition).
2005-09-16 | E-GEOD-3303 | biostudies-arrayexpress
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:Retinal RNA profiles from macula and periphery of each eye were generated by single-cell sequencing. M11-M14 are macula retina and P11-P14 are peripheral retina from the same 78 year old donor. M21-M24 are macula retina and P21-P24 are peripheral retina from the same 90-year-old donor.
2021-08-11 | GSE155288 | GEO
Project description:To comprehensively profile cell types in the human retina, we performed single cell RNA-sequencing on 20,009 cells obtained post-mortem from three donors and compiled a reference transcriptome atlas. Using unsupervised clustering analysis, we identified 18 transcriptionally distinct clusters representing all known retinal cells: rod photoreceptors, cone photoreceptors, Müller glia cells, bipolar cells, amacrine cells, retinal ganglion cells, horizontal cells, retinal astrocytes and microglia.
2019-08-21 | E-MTAB-7316 | biostudies-arrayexpress
Project description:Next-gen RNA sequencing of normal retina, pretumorigenic retina and tumor retinal
| PRJNA681565 | ENA
Project description:The developmental pathway of the neural retina (NR) and retinal pigment epithelium (RPE) has been revealed by extensive research in mice. However, the molecular mechanisms underlying the development of the human NR and RPE, as well as the interactions between these two tissues, have not been well defined. Here, we analyzed 2,421 individual cells from human fetal NR and RPE using single-cell RNA sequencing (RNA-seq) technique and revealed the tightly regulated spatiotemporal gene expression network of human retinal cells. We identified major cell classes of human fetal retina and potential crucial transcription factors for each cell class. We dissected the dynamic expression patterns of visual cycle and ligand-receptor interaction related genes in the RPE and NR. Moreover, we provided a map of disease-related genes for human fetal retinal cells and highlighted the importance of retinal progenitor cells as potential targets of inherited retinal diseases. Our findings captured the key in vivo features of the development of the human NR and RPE and offered insightful clues for further functional studies.
2019-07-04 | GSE107618 | GEO