Human pluripotent stem cell (hPSC)-derived progenies (scRNA-Seq)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA695007 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13553473.fastq.gz | Fastqsanger.gz | |||
| SRR13553474.fastq.gz | Fastqsanger.gz | |||
| SRR13553475.fastq.gz | Fastqsanger.gz | |||
| SRR13553476.fastq.gz | Fastqsanger.gz | |||
| SRR13553477.fastq.gz | Fastqsanger.gz |
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Project description:Human pluripotent stem cell (hPSC)-derived progenies
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Project description:Human pluripotent stem cell (hPSC)-derived progenies (RNA-Seq)
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Project description:The in vitro culture of human cardiac progenitor cells remains a major challenge in biomedicine. The molecular identity of hPSC-derived cardiac progenies and mechanisms controlling their proliferation and differentiation remain unclear. Here, we show that chromatin remodeling and WNT pathway modulation by chemical inhibitors (IQ-1 and CHIR, respectively) synergistically enables stabilization of human cardiac progenitors (SCPs), in a process of transcriptional uncoupling. SCPs are characterized by ISL1pos/KI-67pos/NKX2-5neg expression and are maintained in a quiescent state in the presence of the inhibitors. Upon compound removal, cell autonomous NKX2-5 upregulation hallmarks the recoupling to the cardiomyogenic program, whilst directed differentiation generates endothelial and smooth muscle cells. Chip-sequencing revealed a narrowly defined open chromatin state in SCPs and, when combined with single cell transcriptome analyses, showed a yet unreported Cardiac Neural Crest Cells (CNCCs) footprint. Enforced expression of the oncogene c-MYC could notably not overcome SCPs proliferative quiescence but disrupted the cell autonomous cardiomyogenic potential instead. In contrast, Retinoic Acid (RA) stimulates SCPs proliferation and further supports cells’ phenotypic homogeneity. We consequently show that our in vitro established treatment with IQ1 can also retain ISL1pos cardiac progenies in vivo in a dose and stage specific manner during zebrafish heart development. Due to its chemically defined and reversible nature, our approach provides an unprecedented opportunity to dissect the key mechanisms in cardiac progenitor cell biology, providing a new tool for the advancement of human heart regeneration.
2025-01-27 | GSE165590 | GEO
Project description:The in vitro culture of human cardiac progenitor cells remains a major challenge in biomedicine. The molecular identity of hPSC-derived cardiac progenies and mechanisms controlling their proliferation and differentiation remain unclear. Here, we show that chromatin remodeling and WNT pathway modulation by chemical inhibitors (IQ-1 and CHIR, respectively) synergistically enables stabilization of human cardiac progenitors (SCPs), in a process of transcriptional uncoupling. SCPs are characterized by ISL1pos/KI-67pos/NKX2-5neg expression and are maintained in a quiescent state in the presence of the inhibitors. Upon compound removal, cell autonomous NKX2-5 upregulation hallmarks the recoupling to the cardiomyogenic program, whilst directed differentiation generates endothelial and smooth muscle cells. Chip-sequencing revealed a narrowly defined open chromatin state in SCPs and, when combined with single cell transcriptome analyses, showed a yet unreported Cardiac Neural Crest Cells (CNCCs) footprint. Enforced expression of the oncogene c-MYC could notably not overcome SCPs proliferative quiescence but disrupted the cell autonomous cardiomyogenic potential instead. In contrast, Retinoic Acid (RA) stimulates SCPs proliferation and further supports cells’ phenotypic homogeneity. We consequently show that our in vitro established treatment with IQ1 can also retain ISL1pos cardiac progenies in vivo in a dose and stage specific manner during zebrafish heart development. Due to its chemically defined and reversible nature, our approach provides an unprecedented opportunity to dissect the key mechanisms in cardiac progenitor cell biology, providing a new tool for the advancement of human heart regeneration.
2025-01-27 | GSE165589 | GEO
Project description:The in vitro culture of human cardiac progenitor cells remains a major challenge in biomedicine. The molecular identity of hPSC-derived cardiac progenies and mechanisms controlling their proliferation and differentiation remain unclear. Here, we show that chromatin remodeling and WNT pathway modulation by chemical inhibitors (IQ-1 and CHIR, respectively) synergistically enables stabilization of human cardiac progenitors (SCPs), in a process of transcriptional uncoupling. SCPs are characterized by ISL1pos/KI-67pos/NKX2-5neg expression and are maintained in a quiescent state in the presence of the inhibitors. Upon compound removal, cell autonomous NKX2-5 upregulation hallmarks the recoupling to the cardiomyogenic program, whilst directed differentiation generates endothelial and smooth muscle cells. Chip-sequencing revealed a narrowly defined open chromatin state in SCPs and, when combined with single cell transcriptome analyses, showed a yet unreported Cardiac Neural Crest Cells (CNCCs) footprint. Enforced expression of the oncogene c-MYC could notably not overcome SCPs proliferative quiescence but disrupted the cell autonomous cardiomyogenic potential instead. In contrast, Retinoic Acid (RA) stimulates SCPs proliferation and further supports cells’ phenotypic homogeneity. We consequently show that our in vitro established treatment with IQ1 can also retain ISL1pos cardiac progenies in vivo in a dose and stage specific manner during zebrafish heart development. Due to its chemically defined and reversible nature, our approach provides an unprecedented opportunity to dissect the key mechanisms in cardiac progenitor cell biology, providing a new tool for the advancement of human heart regeneration.
2025-01-27 | GSE165588 | GEO
Project description:The development of human pluripotent stem cell (hPSC)- derived small intestinal organoids (HIOs) has led to an improved understanding of human intestinal development and physiology. HIOs generated using directed differentiation lack some cellular populations found in the native organ, including vasculature. We performed single cell RNA sequencing (scRNA-seq) on approximately 13,000 cells at various timepoints (0, 3, 7, and 14 days) across HIO in vitro development and observed a transient population of endothelial-like cells (ECs) present within HIOs early during differentiation. Our data demonstrate that EC-like cells fail to be robustly maintained in long term culture. Here, we have developed a new directed differentiation approach to enhance co-differentiation and maintenance of ECs within HIOs, leading to the development of vascularized HIOs (vHIOs). scRNAseq was used to compare vHIOs to control HIOs after 59d months in culture.
2020-12-20 | E-MTAB-9228 | biostudies-arrayexpress
Project description:Choroidal atrophy is a common fundus pathological change closely related to the development of age-related macular degeneration (AMD), retinitis pigmentosa, and pathological myopia. Studies suggested that choroidal endothelial cells (CECs) that form the choriocapillaris vessels are the first cells lost in choroidal atrophy. Endothelial cells derived from human pluripotent stem cells (hPSC-ECs) can form blood vessels in vivo and in vitro. We isolated rat choroid and co-cultured with hPSC-ECs. Single-cell RNA-seq (scRNA-seq) studies showed that rat choroid ECs seemed to lose endothelial identity while hPSC-ECs upregulated angiogenesis and hypoxia genes after interacting with choroid.
2024-03-13 | GSE235990 | GEO
Project description:A comprehensive understanding of the human pluripotent stem cell (hPSC) differentiation process stands as a prerequisite for the development hPSC-based therapeutics. In this study, single-cell RNA-sequencing (scRNA-seq) was performed to decipher the heterogeneity during differentiation of three hPSC lines towards corneal limbal stem cells (LSCs). The scRNA-seq data revealed the presence of nine clusters, among which five clusters followed the anticipated differentiation path of LSCs. The remaining four clusters were linked to previously undescribed cell states that were annotated as either mesodermal or undifferentiated subpopulations, and their prevalence was hPSC line-dependent. Distinct cluster-specific marker genes identified in this study were confirmed by immunofluorescence analysis and employed to purify hPSC-derived LSCs, which effectively minimized the variation in the line-dependent differentiation efficiency. In summary, scRNA-seq offered molecular insights into the heterogeneity of hPSC-LSC differentiation, allowing a data-driven strategy to be adopted for consistent and robust generation of LSCs, essential for future advancement toward clinical translation.
2024-06-26 | GSE248496 | GEO
Project description:ScRNA-seq and scATAC-seq analysis of human pluripotent stem cell (hPSC) derived macrophages iMacs
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