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Mus musculus

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

PROVIDER: PRJNA307548 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3081790_1.fastq.gz	Fastqsanger.gz
	SRR3081790_2.fastq.gz	Fastqsanger.gz
	SRR3081800_1.fastq.gz	Fastqsanger.gz
	SRR3081800_2.fastq.gz	Fastqsanger.gz
	SRR3081810_1.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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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

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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]

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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]

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

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