Mapping human pluripotent stem cell differentiation pathways via high throughput single-cell RNA-sequencing
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ABSTRACT:
PROVIDER: PRJNA420514 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6335130_1.fastq.gz | Fastqsanger.gz | |||
| SRR6335130_2.fastq.gz | Fastqsanger.gz | |||
| SRR6335140_1.fastq.gz | Fastqsanger.gz | |||
| SRR6335140_2.fastq.gz | Fastqsanger.gz | |||
| SRR6335131_1.fastq.gz | Fastqsanger.gz |
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Project description:Human pluripotent stem cells (hPSCs) provide both powerful models for studying cellular differentiations, and unlimited sources of cells for regenerative medicine. However, a comprehensive single cell level differentiation roadmap for hPSCs has not been achieved yet. Here, we used high throughput single-cell RNA-sequencing (scRNA-seq) method, based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body (EB) system. We presented a cellular landscape for hPSC early differentiations covering different cellular lineages, including neural cell, muscle cell, endothelial cell, stromal cell, liver cell, and epithelial cell. Through pseudotemporal analysis, we constructed the differentiation trajectories of these progenitor cells and revealed the gene expression dynamics in the process of differentiation. We reset Primed H9 into Naïve-like H9 and studied cell state transition process via scRNA-seq. We found that mesendoderm genes are enriched in Naïve-like H9. Functionally, Naïve-like H9 showed better potency for differentiation into the hematopoietic lineages. We constructed the differentiation landscape of hPSC early differentiation by scRNA-seq analysis. We offer new insights into molecular pathways of early embryonic lineages that can be harnessed for optimization of differentiation protocols. (Pipeline for C1 data demultiplex : https://github.com/bioeauty/sccpipe)
2018-03-06 | GSE107552 | GEO
Project description:BackgroundHuman pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differentiation roadmap for hPSCs has not been achieved.ResultsWe use high throughput single-cell RNA-sequencing (scRNA-seq), based on optimized microfluidic circuits, to profile early differentiation lineages in the human embryoid body system. We present a cellular-state landscape for hPSC early differentiation that covers multiple cellular lineages, including neural, muscle, endothelial, stromal, liver, and epithelial cells. Through pseudotime analysis, we construct the developmental trajectories of these progenitor cells and reveal the gene expression dynamics in the process of cell differentiation. We further reprogram primed H9 cells into naïve-like H9 cells to study the cellular-state transition process. We find that genes related to hemogenic endothelium development are enriched in naïve-like H9. Functionally, naïve-like H9 show higher potency for differentiation into hematopoietic lineages than primed cells.ConclusionsOur single-cell analysis reveals the cellular-state landscape of hPSC early differentiation, offering new insights that can be harnessed for optimization of differentiation protocols.
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