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Homo sapiens

ABSTRACT: Changes in global nucleosome positioning during human embryonic stem cell differentiation

PROVIDER: PRJNA196743 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR830684_1.fastq.gz	Fastqsanger.gz
	SRR830684_2.fastq.gz	Fastqsanger.gz
	SRR831188_1.fastq.gz	Fastqsanger.gz
	SRR831188_2.fastq.gz	Fastqsanger.gz
	SRR832927_1.fastq.gz	Fastqsanger.gz

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Genome-wide nucleosome positioning during embryonic stem cell development

Project description:This SuperSeries is composed of the following subset Series: GSE40910: Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq] GSE40948: Genome-wide nucleosome positioning during embryonic stem cell development [RNA-Seq] GSE40951: Genome-wide nucleosome positioning during embryonic stem cell development [ChIP-Seq] Refer to individual Series

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Project description:Metabolism is vital to cellular function and tissue homeostasis during human lung development. In utero, embryonic pluripotent stem cells undergo endodermal differentiation towards a lung progenitor cell fate that can be mimicked in vitro using induced human pluripotent stem cells (hiPSCs) to study genetic mutations. To identify differences between wild type and surfactant protein B (SFTPB)-deficient cell lines during endoderm specification towards lung, we used an untargeted metabolomics approach to evaluate the developmental changes in metabolites. We found that the metabolites most enriched during the differentiation from pluripotent stem cell to lung progenitor cell, regardless of cell line, were sphingomyelins and phosphatidylcholines, two important lipid classes in fetal lung development. The SFTPB mutation had no metabolic impact on early endodermal lung development. The identified metabolite signatures during lung progenitor cell differentiation may be utilized as biomarkers for normal embryonic lung development.

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Project description:Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq]

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Project description:Genome-wide nucleosome positioning during embryonic stem cell development [RNA-Seq]

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Genome-wide nucleosome positioning during embryonic stem cell development [MNase-Seq]

Project description:We determined genome-wide nucleosome occupancy in mouse embryonic stem cells and their neural progenitor and embryonic fibroblast counterparts to assess features associated with nucleosome positioning during lineage commitment. Cell type and protein specific binding preferences of transcription factors to sites with either low (e.g. Myc, Klf4, Zfx) or high (e.g. Nanog, Oct4 and Sox2) nucleosome occupancy as well as complex patterns for CTCF were identified. Nucleosome depleted regions around transcription start and termination sites were broad and more pronounced for active genes, with distinct patterns for promoters classified according to their CpG-content or histone methylation marks. Throughout the genome nucleosome occupancy was dependent on the presence of certain histone methylation or acetylation modifications. In addition, the average nucleosome-repeat length increased during differentiation by 5-7 base pairs, with local variations for specific genomic regions. Our results reveal regulatory mechanisms of cell differentiation acting through nucleosome repositioning. We have determined genome-wide nucleosome position maps in mouse embryonic stem cells (ESCs), neural progenitor cells (NPCs) derived from these ESCs by retinoic acid induced differentiation as well as mouse embryonic fibroblasts (MEFs) from the corresponding mouse strain

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Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation - gene expression

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