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Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

ABSTRACT: Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

PROVIDER: PRJNA128663 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR064650.fastq.gz	Fastqsanger.gz
	SRR064651.fastq.gz	Fastqsanger.gz
	SRR064652.fastq.gz	Fastqsanger.gz
	SRR064653.fastq.gz	Fastqsanger.gz
	SRR064654.fastq.gz	Fastqsanger.gz

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Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

Project description:This SuperSeries is composed of the following subset Series: GSE23402: Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (Affymetrix) GSE23455: Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (ChIP-seq) Refer to individual Series

2010-08-08 | E-GEOD-22499 | biostudies-arrayexpress

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (Affymetrix)

Project description:Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells should provide a robust means to assess whether the genomes of these cells have similar pluripotent states. Recent studies have suggested that ES and iPS cells represent different pluripotent states with substantially different gene expression profiles. We describe here a comparison of global chromatin structure and gene expression data for a panel of human ES and iPS cells. Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ES and iPS cells with respect to these marks. Gene expression profiles confirm that the transcriptional programs of ES and iPS cells show very few consistent differences. Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ES from iPS cells. Examination of gene expression in 7 human ES cell lines, 8 human iPS cell lines, and 2 fibroblast cell line2.

2010-08-09 | E-GEOD-23402 | biostudies-arrayexpress

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (ChIP-seq)

Project description:Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells should provide a robust means to assess whether the genomes of these cells have similar pluripotent states. Recent studies have suggested that ES and iPS cells represent different pluripotent states with substantially different gene expression profiles. We describe here a comparison of global chromatin structure and gene expression data for a panel of human ES and iPS cells. Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ES and iPS cells with respect to these marks. Gene expression profiles confirm that the transcriptional programs of ES and iPS cells show very few consistent differences. Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ES from iPS cells. Examination of two histone modifications (H3K4me3 and H3K27me3) in 6 human ES cell lines, 8 human iPS cell lines, and 1 fibroblast cell line.

2010-08-09 | E-GEOD-23455 | biostudies-arrayexpress

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (Affymetrix)

2010-08-09 | GSE23402 | GEO

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (ChIP-seq)

2010-08-09 | GSE23455 | GEO

Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

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Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells.

Project description:Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) should provide a robust means to assess whether the genomes of these cells have similar pluripotent states. Recent studies have suggested that ESCs and iPSCs represent different pluripotent states with substantially different gene expression profiles. We describe here a comparison of global chromatin structure and gene expression data for a panel of human ESCs and iPSCs. Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ESCs and iPSCs with respect to these marks. Gene expression profiles confirm that the transcriptional programs of ESCs and iPSCs show very few consistent differences. Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ESCs from iPSCs.

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Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells in vivo

Project description:Induced pluripotent stem cells (iPSCs) hold great promise for regenerative medicine, but genetic instability is a major concern. Embryonic pluripotent cells also accumulate mutations during early development, but how this relates to the mutation burden in iPSCs remains unknown. Here, we directly compared the mutation burden of cultured iPSCs with their isogenic embryonic cells during human embryogenesis. We generated developmental lineage trees of human fetuses by phylogenetic inference from somatic mutations in the genomes of multiple stem cells, which were derived from different germ layers. Using this approach, we characterized the mutations acquired pre-gastrulation and found a rate of 1.65 mutations per cell division. When cultured in hypoxic conditions, iPSCs generated from fetal stem cells of the assessed fetuses displayed a similar mutation rate and spectrum. Our results show that iPSCs maintain a genomic integrity during culture at a similar degree as their pluripotent counterparts do in vivo.

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