Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE97988 | GEO | 2018/04/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

2018-04-18 | GSE97989 | GEO

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

2018-04-18 | GSE97991 | GEO

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

2018-04-18 | GSE97990 | GEO

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

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

| PRJNA383580 | ENA

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-04-18 | GSE97992 | GEO

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.

2013-11-04 | GSE38216 | GEO

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

2013-11-04 | GSE38214 | GEO

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

2013-11-04 | E-GEOD-38216 | biostudies-arrayexpress

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

2013-11-04 | E-GEOD-38214 | biostudies-arrayexpress

TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer [CMS-IP]

Project description:TET enzymes are dioxygenases that promote DNA demethylation by oxidizing the methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Here we report a close correspondence between 5hmC-marked regions, chromatin accessibility and enhancer activity in B cells, and a strong enrichment for consensus binding motifs for basic region-leucine zipper (bZIP) transcription factors at TET-responsive genomic regions. Functionally, Tet2 and Tet3 regulate class switch recombination (CSR) in murine B cells by enhancing expression of Aicda, encoding the cytidine deaminase AID essential for CSR. TET enzymes deposit 5hmC, demethylate and maintain chromatin accessibility at two TET-responsive elements, TetE1 and TetE2, located within a superenhancer in the Aicda locus. Transcriptional profiling identified BATF as the bZIP transcription factor involved in TET-dependent Aicda expression. 5hmC is not deposited at TetE1 in activated Batf-deficient B cells, indicating that BATF recruits TET proteins to the Aicda enhancer. Our data emphasize the importance of TET enzymes for bolstering AID expression, and highlight 5hmC as an epigenetic mark that captures enhancer dynamics during cell activation.

2019-04-29 | GSE116201 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data