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Mus musculus

ABSTRACT: Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [ChIP-Seq]

PROVIDER: PRJNA307549 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3081750.fastq.gz	Fastqsanger.gz
	SRR3081760.fastq.gz	Fastqsanger.gz
	SRR3081770.fastq.gz	Fastqsanger.gz
	SRR3081751.fastq.gz	Fastqsanger.gz
	SRR3081761.fastq.gz	Fastqsanger.gz

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Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming

Project description:Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming

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Project description:Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [Expression]

| PRJNA307547 | ENA

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Project description:Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [HiC-Seq]

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Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [ChIP-Seq]

Project description:We studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale TAD repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic cell specific genome structures while establishing an embryonic stem cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable discerning their cell-of-origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin dependent gene expression patterns. ChIPseq for CTCF and H3K27ac was performed on early and late iPS cells derived from different founders

2016-03-01 | E-GEOD-76478 | biostudies-arrayexpress

Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [Expression]

Project description:We studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale TAD repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic cell specific genome structures while establishing an embryonic stem cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable discerning their cell-of-origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin dependent gene expression patterns. Transcriptome analysis was performed in somatic cells (NSC, macrophages, MEFs and pre-B cells) and their corresponding early and late induced pluripotent stem cells. In addition, expression analysis was performed in E14 embryonic stem cells

2016-03-01 | E-GEOD-76480 | biostudies-arrayexpress

Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [HiC-Seq]

Project description:We studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale TAD repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic cell specific genome structures while establishing an embryonic stem cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable discerning their cell-of-origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin dependent gene expression patterns. Hi-C was performed in somatic cells (NSC, macrophages, MEFs and pre-B cells) and their corresponding early and late induced pluripotent stem cells. In addition Hi-C was performed in E14 embryonic stem cells

2016-03-01 | E-GEOD-76479 | biostudies-arrayexpress

Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [Expression]

2016-03-01 | GSE76480 | GEO

Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [HiC-Seq]

2016-03-01 | GSE76479 | GEO

Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [ChIP-Seq]

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Reprogramming-associated aberrant DNA methylation determines hematopoietic differentiation capacity of human induced pluripotent stem cells [parental_lines_expression]

Project description:The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. In contrast, maturation capacity (hematopoietic precursors to mature blood) is affected by iPSC origin; blood-derived iPSCs showed the highest capacity. However, some fibroblast-derived iPSCs showed higher capacity than blood-derived clones. Tracking of DNA methylation changes during reprogramming reveals that maturation capacity is highly associated with aberrant DNA methylation acquired during reprogramming, rather than the types of iPSC origins. These data demonstrated that variations in the hematopoietic differentiation capacity of iPSCs are not attributable to somatic memories of their origins. Expression analysis of parental somatic tissues of human iPSCs used for the present study.

2016-06-29 | E-GEOD-73629 | biostudies-arrayexpress

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