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Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses (scRNA-seq)

ABSTRACT: Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses (scRNA-seq)

PROVIDER: PRJNA892988 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22006800.fastq.gz	Fastqsanger.gz
	SRR22006801.fastq.gz	Fastqsanger.gz
	SRR22006802.fastq.gz	Fastqsanger.gz
	SRR22006803.fastq.gz	Fastqsanger.gz
	SRR22006805.fastq.gz	Fastqsanger.gz

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Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses

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Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses.

Project description:In vivo differentiation of human pluripotent stem cells (hPSCs) has unique advantages, such as multilineage differentiation, angiogenesis, and close cell-cell interactions. To systematically investigate multilineage differentiation mechanisms of hPSCs, we constructed the in vivo hPSC differentiation landscape containing 239,670 cells using teratoma models. We identified 43 cell types, inferred 18 cell differentiation trajectories, and characterized common and specific gene regulation patterns during hPSC differentiation at both transcriptional and epigenetic levels. Additionally, we developed the developmental single-cell Basic Local Alignment Search Tool (dscBLAST), an R-based cell identification tool, to simplify the identification processes of developmental cells. Using dscBLAST, we aligned cells in multiple differentiation models to normally developing cells to further understand their differentiation states. Overall, our study offers new insights into stem cell differentiation and human embryonic development; dscBLAST shows favorable cell identification performance, providing a powerful identification tool for developmental cells.

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Project description:Single cell genome, DNA methylome, and transcriptome sequencing has been achieved separately. However, to analyze the regulation of RNA expression by genetic and epigenetic factors within an individual cell, it is necessary to analyze these omics simultaneously from the same single cell. Here we developed a single cell triple omics sequencing technique- scTrio-seq, to analyze the genome, DNA methylome, and transcriptome concurrently of a mammalian cell. 6 single human HepG2 cell line cells were sequenced using the newly developed scTrio-seq, other 2 HepG2 cells were sequenced using scRNA-seq and other 2 HepG2 cells were sequenced using scRRBS as technique control. 6 single mouse embryonic stem cells (mESCs) were sequenced using the newly developted scTrio-seq. Meanwhile, two scRNA-seq and two scRRBS were also completed using two mESCs separately. 26 single cells from hepatocellular carcinoma were sequenced using scTrio-seq to analyze the regulation relations between three omics of cancer cells.

2016-03-01 | E-GEOD-65364 | biostudies-arrayexpress

Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses (scATAC-seq)

Project description:In vivo differentiation of human pluripotent stem cells (hPSCs) has unique advantages such as multilineage differentiation, angiogenesis, and close cell‒cell interactions. To systematically investigate the multilineage differentiation mechanisms of hPSCs, we constructed the in vivo hPSC differentiation landscape containing 239,670 cells using teratoma models. We inferred 18 cell differentiation trajectories and characterized common and specific gene regulation patterns during hPSC differentiation at both transcriptional and epigenetic levels. The results of developing single cell Basic Local Alignment Search Tool (dscBLAST), our self-developed tool for cell identification and developmental stage speculation, further confirmed the differentiated cell identity and suggested that cells in the teratoma are largely at immature developmental stages. Overall, our study offers new insights into stem cell fate decisions and embryonic development; dscBLAST shows favorable cell identification performance, providing both developmental and adult cells with a powerful tool for cell annotation and stage speculation.

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