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Single-cell gene expression profiles of hESC-derived retinal organoid progenitor cells and photoreceptor precursors from deep full-length scRNA-seq.

ABSTRACT: Single-cell gene expression profiles of hESC-derived retinal organoid progenitor cells and photoreceptor precursors from deep full-length scRNA-seq.

PROVIDER: PRJNA857290 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20068500_1.fastq.gz	Fastqsanger.gz
	SRR20068500_2.fastq.gz	Fastqsanger.gz
	SRR20068600_1.fastq.gz	Fastqsanger.gz
	SRR20068600_2.fastq.gz	Fastqsanger.gz
	SRR20068700_1.fastq.gz	Fastqsanger.gz

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Single-cell gene expression profiles of hESC-derived retinal organoid progenitor cells and photoreceptor precursors from deep full-length scRNA-seq.

Project description:Human retinal organoids have been invaluable in vitro models of retinal development and disease. To investigate whether cell states and gene expression changes observed in human fetal cone development are accurately replicated in organoids, we produced H9 hESC-derived retinal organoids using two published methods (Kuwahara et al. 2015, Nat Comm 6, 6286, https://doi.org/10.1038/ncomms7286; Zhong et al. 2014, Nat Comm 5, 4047, https://doi.org/10.1038/ncomms5047). We then FACS-enriched cone and rod precursors and retinal progenitor cells every two weeks from 55-140 DIC, as well as at 225 DIC, and performed deep, full-length scRNA-seq chemistry. These data were used to identify maturation differences related to the organoid production method, identify aberrant cell populations or gene expression timing relative to human fetal retina, and define cone and rod photoreceptor trajectories in the retinal organoid setting.

2023-02-01 | GSE207824 | GEO

Single-cell gene expression profiles of human retinal progenitor cells and photoreceptor precursors from deep full-length scRNA-seq.

Project description:The human retina has unique features that are not all fully replicated in animal models. Several human-specific features center on cone photoreceptors such as a cone-rich fovea, three cone types, and the cone precursor’s proliferative response to RB1 loss. Prior droplet-based single cell RNA-sequencing (scRNA-seq) datasets have not clearly defined cone precursor developmental states or gene expression patterns. To further elucidate photoreceptor developmental trajectories, we FACS-enriched cone and rod precursors and retinal progenitor cells from eighteen Fetal Week 13-19 retina and performed deep, full-length scRNA-seq. These data were used to evaluate post-mitotic photoreceptor precursor trajectories, accompanying gene expression changes, and cone-specific features that drive the cone precursor proliferative response.

2023-01-01 | GSE207802 | GEO

Resolving fate bifurcation of photoreceptor precursor in human retinal organoid by single-cell transcriptomics

Project description:Cone and rod photoreceptors in human enable daytime color and nighttime dark vision respectively and abnormality in photoreceptor development results in blindness. However, when and how the two photoreceptors are fate-determined during development is largely unknown. Herein, we established a cell atlas for human photoreceptor development, based on single-cell transcriptomic profiling of engineered human retinal organoids engineered to trace the photoreceptor lineages during developmentto monitor the photoreceptor lineages during development. For the first time, we demonstrated the subtypes of photoreceptor precursors based on unsupervised clustering of single-cell transcriptomesbifurcation of cell fate in the photoreceptor precursors, withwith the conespecific expression of molecular marker gene PDE6H ands for cone precursor and rod marker gene NR2E3 differentially expressed among others precursor. Further dissection of transcriptional segregation of the two precursors uncovered PHLDA1 as an intrinsic regulator intrinsic regulator in the fate bifurcation of of the rod-related gene networksphotoreceptor subtypes. Photoreceptor precursors with decreased PHLDA1 yield more cones while reduced the number of rods. The PHLDA1-mediated modification of cell fate can be directed downstream of IGF1 signaling, and exhibited an inhibitory effect on AKT phosphorylation which was associated with cone differentiation., which directed the downstream effects of IGF1 to promote the rod differentiation. Collectively, our data identified PHLDA1 as a novel regulator of fate determination of photoreceptors at the precursor stage, andour study shed lights on the cellular and molecular mechanisms of human photoreceptor precursor specification, and provided a framework to study mechanisms of cell fate determination of human retinal cells.

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Photoreceptor precursors derived from 3D cultures of embryonic stem cells mature and integrate in degenerate retina

Project description:To isolate photoreceptor precursors fit for transplantation, we adapted a 3D differentiation protocol that generates neuroretina from mouse ES cells. We used an adeno-associated viral vector (pseudotype2/9)carrying a GFP reporter under the control of a Rhodopsin promoter (AAV2/9.Rhop.GFP)to select rod precursors. AAV2/9.Rhop.GFP+ rods were sorted at days 26 and 34 and post natal day P12.

2013-07-17 | E-MEXP-3921 | biostudies-arrayexpress

Single-cell gene expression profiles of human retinal progenitor cells and photoreceptor precursors from deep full-length scRNA-seq.

Project description:Single-cell gene expression profiles of human retinal progenitor cells and photoreceptor precursors from deep full-length scRNA-seq.

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Stable STIM1 knockdown in human neural precursors derived from hESC line, H9

Project description:Stable STIM1 knockdown in human neural precursors derived from hESC line, H9

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Effective transplantation of photoreceptor precursor cells selected via cell surface antigen expression.

Project description:Microarray analysis of postnatal NrlGFP-expressing rod photoreceptor precursors. NrlGFP positive versus NrlGFP negative at postnatal day 4

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Gene expression analysis of embryonic photoreceptor precursor cells using BAC-Crx-EGFP transgenic mouse.

Project description:We generated a transgenic mouse line which express EGFP in the retina driven by the Crx promoter using BAC transgenesis. We sorted EGFP-positive photoreceptor precursors at E17.5 using FACS, and subsequently performed microarray analysis of the FACS-sorted cells. In order to clarify a molecular role of Crx in developing cone photoreceptor precursors, we investigated the expression profile of the BAC-Crx-EGFP-positive cells compared with that of the BAC-Crx-EGFP-negative cells at E17.5.

2010-12-25 | E-GEOD-25607 | biostudies-arrayexpress

Single cell RNA-seq of CRX+ cells obtained at day 90 of retinal organoid differentiation

Project description:Death of photoreceptors and/or Retinal Pigment Epithelium (RPE) cells is a common cause of age related and inherited retinal dystrophies, thus their replenishment from renewable stem cell sources is a well sought therapeutic goal. Human pluripotent stem cells provide a useful cell source in view of their limitless self-renewal capacity and potential to differentiate into all key retinal cell types either in isolation or as part of three dimensional retinal organoids. Photoreceptor precursors have been isolated from differentiating human pluripotent stem cells either through application of cell surface markers or fluorescent reporter approaches and shown to share a transcriptional profile akin to foetal photoreceptors. In this study we investigated the transcriptional profile of CRX+ photoreceptor precursors derived from human embryonic stem cells (hESC) using single cell RNA sequencing and their engraftment capacity in an animal model of retinitis pigmentosa (C3H/rd1). Single cell RNA seq analysis revealed the presence of dominant cell cluster which displayed the hallmarks of early cone photoreceptor expression. When transplanted subretinally into the C3H/rd1 mice, the Crx positive cells settled next to the inner nuclear layer of host retina, matured into cone photoreceptors and made connections with the inner neurones of the host retina. Cellular transfer between the host retina and donor photoreceptors was investigated and shown to be minimal. Together our data provide valuable molecular insights into the transcriptional profile of human pluripotent stem cells derived CRX+ photoreceptor precursors and indicate their usefulness as a source of transplantable cone photoreceptors.

2019-04-01 | GSE112507 | GEO

Control or KZFP KD hESC-derived organoids RNA-seqs

Project description:Control or KD hESC were differentiated into organoids as decribed in Methods. RNA was extracted from individual organoids at day 20 after commencing the STEMdiff™ Cerebral Organoid Kit protocol. Day 0 was designated as the day of transfer of hESC to a 96-well plate for differentiation into embryoid bodies .

2020-02-18 | GSE145406 | GEO

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