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Homo sapiens

ABSTRACT: 5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (ATAC-Seq)

PROVIDER: PRJNA383583 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5459170_1.fastq.gz	Fastqsanger.gz
	SRR5459170_2.fastq.gz	Fastqsanger.gz
	SRR5459171_1.fastq.gz	Fastqsanger.gz
	SRR5459171_2.fastq.gz	Fastqsanger.gz
	SRR5459172_1.fastq.gz	Fastqsanger.gz

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5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation

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Project description:5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (RNA-Seq)

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5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (RNA-Seq)

Project description:We generated 5hmC, WGBS and RNAseq of the cells in 5 stages during hES-to-pancreatic endoderm cell differantiation, and investigated the 5hmC correlation with 4 histones (H3K4me1, H3K4me3, H3K27ac and H3K27me3) during this process. Our results showed that 5hmC is dynamically correlate with enhancers' activities.

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5hmC dynamically correlated with enhancer's activities during hES-to-Pancreatic endoderm cell differentiation (ATAC-Seq)

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Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cells (Methylation BeadChip)

Project description:DNA methylation and hydroxymethylation have been implicated in normal development and differentiation, but our knowledge about the genome-wide distribution of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) during cellular differentiation remains limited. Using in vitro model system of gradual differentiation of human embryonic stem (hES) cells into ventral midbrain-type neural precursor (NP) cells and terminally into dopamine (DA) neurons, we explored changes in 5mC or 5hmC patterns during lineage commitment. We used three techniques, 450K DNA methylation array, MBD-seq, and hMeDIP-seq, and found combination of these methods can provide comprehensive information on the genome-wide 5mC or 5hmC patterns. We observed dramatic changes of 5mC patterns during differentiation of hES cells into NP cells. Although genome-wide 5hmC distribution was more stable than 5mC, coding exons, CpG islands and shores showed dynamic 5hmC patterns during differentiation. In addition to the role of DNA methylation as a mechanism to initiating gene silencing, we also found DNA methylation as a locking system to maintain gene silencing. More than 1,000 genes including mesoderm development related genes acquired promoter methylation during neuronal differentiation even though they were already silenced in hES cells. Finally, we found that activated genes lost 5mC in transcription start site (TSS) but acquired 5hmC around TSS and gene body during differentiation. Our findings may provide clues for elucidating the molecular mechanisms underlying lineage specific differentiation of pluripotent stem cells during human embryonic development.

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Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cell (hMeDIP-Seq and MBD-Seq)

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