ScATAC-seq of early brain organoid development from pluripotency
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ABSTRACT:
PROVIDER: PRJEB55274 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.
2022-08-18 | E-MTAB-11998 | biostudies-arrayexpress
Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.
2022-08-18 | E-MTAB-12001 | biostudies-arrayexpress
Project description:scRNA-seq of early brain organoid development from pluripotency
| PRJEB55271 | ENA
Project description:In order to provide multi-omic resolution to human retinal organoid developmental dynamics, we performed scRNA-seq and scATAC-seq from the same cell suspension across a time course (6-46 weeks) of human retinal organoid development. This data set covers all the retinal organoid scATAC-seq data generated from IMR90 and 409B2-iCas9 cell lines.
2023-03-12 | E-MTAB-12714 | biostudies-arrayexpress
Project description:In order to provide multi-omic resolution to human retinal organoid developmental dynamics, we performed scRNA-seq and scATAC-seq from the same cell suspension across a time course (6-46 weeks) of human retinal organoid development. This data set covers all the retinal organoid scRNA-seq data generated from IMR90 and409B2-iCas9 cell lines.
2023-03-12 | E-MTAB-12715 | biostudies-arrayexpress
Project description:Defining molecular controls that orchestrate human brain development is essential for uncovering the complexity behind neurodevelopment and the pathogenesis of neurological disorders. Due to the difficulties in accessing embryonic and fetal brain tissues, the differentiation of human pluripotent stem cell (hPSC)-derived three-dimensional neural organoids has made it possible to recapitulate this developmental process in vitro and provide a unique opportunity to investigate human brain development and disease. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the initial stages of pluripotency and neural differentiation towards the formation of cerebral organoids. Our integrative analysis uncovers key phospho-signalling events underlying neural lineage differentiation, and their convergence on transcriptional (co-)factors and chromatin remodellers that govern downstream gene regulatory networks (GRNs). Comparative analysis with developing human and mouse embryos using these GRNs demonstrates the fidelity of our early cerebral organoids in modelling embryonic brain development. Finally, we demonstrate biochemical modulation of the AKT signalling as a key molecular switch for controlling human cerebral organoid formation. Our data provides a comprehensive resource to gain insight into the molecular controls in human embryonic brain development and also provide a guide for future development of protocols for human cerebral organoid differentiation.
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Project description:Organoids enable disease modeling in complex and structured human tissue, in vitro. Like most 3D cultures, they lack sufficient oxygen supply, leading to cellular stress. These negative effects are particularly prominent in complex models, like brain organoids, where they can prevent proper lineage commitment. Here, we analyze brain organoid and fetal single cell RNA sequencing (scRNAseq) data from published and new datasets totaling about 190,000 cells. We describe a unique stress signature found in all organoid samples, but not in fetal samples. We demonstrate that cell stress is limited to a defined organoid cell population, and present Gruffi, an algorithm that uses granular functional filtering to identify and remove stressed cells from any organoid scRNAseq dataset in an unbiased manner and validate our findings on six further datasets from different organoid protocols and early brains. Our data show that adverse effects of cell stress can be corrected by bioinformatic analysis, improving developmental trajectories and resemblance to fetal data.
2022-06-06 | GSE205554 | GEO
Project description:Defining molecular controls that orchestrate human brain development is essential for uncovering the complexity behind neurodevelopment and the pathogenesis of neurological disorders. Due to the difficulties in accessing embryonic and fetal brain tissues, the differentiation of human pluripotent stem cell (hPSC)-derived three-dimensional neural organoids has made it possible to recapitulate this developmental process in vitro and provide a unique opportunity to investigate human brain development and disease. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the initial stages of pluripotency and neural differentiation towards the formation of cerebral organoids. Our integrative analysis uncovers key phospho-signalling events underlying neural lineage differentiation, and their convergence on transcriptional (co-)factors and chromatin remodellers that govern downstream gene regulatory networks (GRNs). Comparative analysis with developing human and mouse embryos using these GRNs demonstrates the fidelity of our early cerebral organoids in modelling embryonic brain development. Finally, we demonstrate biochemical modulation of the AKT signalling as a key molecular switch for controlling human cerebral organoid formation. Our data provides a comprehensive resource to gain insight into the molecular controls in human embryonic brain development and also provide a guide for future development of protocols for human cerebral organoid differentiation.
2024-04-21 | GSE248901 | GEO
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 | GSE235577 | GEO