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Genome-wide transcriptome analysis of pluripotent (2iL) and differentiated (2iL withdrawal) mES cells, overexpressing a DOX-inducible Esrrb

ABSTRACT: Genome-wide transcriptome analysis of pluripotent (2iL) and differentiated (2iL withdrawal) mES cells, overexpressing a DOX-inducible Esrrb

PROVIDER: PRJNA763238 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15900287.fastq.gz	Fastqsanger.gz
	SRR15900288.fastq.gz	Fastqsanger.gz
	SRR15900289.fastq.gz	Fastqsanger.gz
	SRR15900290.fastq.gz	Fastqsanger.gz
	SRR15900291.fastq.gz	Fastqsanger.gz

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Genome-wide transcriptome analysis of pluripotent (2iL) and differentiated (2iL withdrawal) mES cells, overexpressing a DOX-inducible Esrrb

Project description:We report the application of genome-wide RNA-sequencing analysis for pluripotent mouse ES cells transfected with DOX-inducible Esrrb and maintained in 2iL, or differentiated for 96 hours with or without Doxycycline. We find that Esrrb expression is sufficient to confer reversibility and activates both naive and formative genes.

2023-01-25 | GSE184132 | GEO

Genome-wide transcriptome analysis of pluripotent (2iL) or differentiated (2iL withdrawal) wild-type or Esrrb KO mES cells.

Project description:Genome-wide transcriptome analysis of pluripotent (2iL) or differentiated (2iL withdrawal) wild-type or Esrrb KO mES cells.

| PRJNA763237 | ENA

Genome-wide transcriptome analysis of pluripotent (2iL) or differentiated (2iL withdrawal) wild-type or Esrrb KO mES cells.

Project description:We report the application of genome-wide RNA-sequencing analysis for pluripotent wild-type or Esrrb KO mouse ES cells, maintained in 2iL or differentiated for 24, 48 or 72 hours. We find an anticipated progression of Esrrb KO cells as compared to wild-type cells and a massive downregulation of formative genes in multiple Esrrb KO clones, confirming the role of Esrrb as an inducer of the formative program. Such Esrrb KO cells also show upregulation of committed genes and activation of the Mesendoderm program.

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Genome-wide maps of ESRRB binding in pluripotent (2iL) and differentiated (48h, 96h) mES cells

Project description:We report the application of sequencing technology for profiling of genome-wide ESRRB binding in mouse ES cells. We generated genome-wide chromatin-state maps of mouse embryonic stem cells maintained in pluripotent state (2iL) and differentiated for 48 and 96 hours (48 and 96). We find that the large majority of ESRRB binding occurs in 2iL and at 48 hours and that several formative genes promoters are bound by ESRRB in 2iL and at 48h. Moreover ESRRB peaks on naïve genes (e.g. Tfcp2l1, Nanog) decrease as soon as cells start differentiating while peaks on formative genes are present in 2iL and the signal is maintained (or increased) at 48 hours, further endorsing the concept of Esrrb as a direct activator of the formative gene program during the Reversible phase.

2023-01-25 | GSE184131 | GEO

Genome-wide transcriptome analysis of pluripotent (2iL), differentiated (2iL withdrawal) or re-induced (2iL re-application during differentiation) mES cells

Project description:Genome-wide transcriptome analysis of pluripotent (2iL), differentiated (2iL withdrawal) or re-induced (2iL re-application during differentiation) mES cells

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Genome-wide transcriptome analysis of pluripotent (2iL), differentiated (2iL withdrawal) or re-induced (2iL re-application during differentiation) mES cells

Project description:We report the application of genome-wide RNA-sequencing analysis for pluripotent mouse ES cells maintained in 2iL, differentiated for 24, 48, 96 and 120 hours or treated with 2iL for 24hours after 48 or 96 hours of differentiation. We find that after 48h of differentiation cells respond to 2iL reinduction by upregulating naïve markers and downregulating formative markers, while cells that underwent 96 hours of differentiation failed to do so. This indicates that committment is associated with a change in the transcriptional response to external signals.

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Genome-wide maps of ESRRB binding in pluripotent (2iL) and differentiated (48h, 96h) mES cells

Project description:Genome-wide maps of ESRRB binding in pluripotent (2iL) and differentiated (48h, 96h) mES cells

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Genome-wide maps of chromatin accessible regions in pluripotent (2iL) and differentiated (48h, 96h) mES cells

Project description:We report the application of sequencing technology for profiling of genome-wide chromatin accessible regions in mouse ES cells. We generated genome-wide chromatin-state maps of mouse embryonic stem cells maintained in pluripotent state (2iL) and differentiated for 48 and 96 hours (48 and 96). We find that the large majority of ESRRB motif-cointaining regions are found in 2iL and at 48 hours and that several formative genes contain time-specific oper regions at 48h, but not at earlier or later time-points.

2023-01-25 | GSE184130 | GEO

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Project description:We report the application of genome-wide RNA-sequencing analysis for pluripotent mouse ES cells maintained in 2iL or 2i and differentiated for 12, 24, 36, 48, 60, 72, 84, 96 hours. We find that cells differentiating from both 2iL and 2i follow a similar trajectory with 2i samples accelerated by 24 hours. Moreover we performed unsupervised hierarchical clustering on cells differentiating from 2iL and defined 6 groups of genes (gene signatures) based on their transcriptional behaviour during differentiation. Finally we reported that only after activation and dissolution of the formative signatures cells are fully committed. The same behaviour is true for cells differentiating from 2i.

2023-01-25 | GSE184134 | GEO

Genome-wide transcriptome analysis of Esrrb WT and conditional Esrrb KO mouse embryonic stem cells

Project description:We report the application of genome-wide RNA-sequencing analysis for Esrrb WT and conditional Esrrb KO mES cells after differentation for 48 hours. Global transcriptome profiling revealed impaired induction of formative genes in conditional KO cells compared to WT cells.

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