Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA methylation and gene expression changes during human embryonic stem cell differentiation

ABSTRACT: Investigate the genome-wide DNA methylation and gene expression changes during human embryonic stem cell differentiation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE32371 | GEO | 2011/09/26

SECONDARY ACCESSION(S): PRJNA147971

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

DNA methylation and gene expression changes during human embryonic stem cell differentiation

Project description:Investigate the genome-wide DNA methylation and gene expression changes during human embryonic stem cell differentiation. hESCs (H1 and H13) DNA samples for 3 different differentian stage (D0, undifferentiated;D21, 21 days after undirected differentiation; D90, 90 days after undirected differentiation); two-color experiment, paired comparison (differentiated vs undifferentiated; A & B: two biological replicates). Differentian-stage variation in methylation profiling of human DNA samples were detected by MSAM. 2µg of DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification. Analysis of differentian-stage variation in gene expression of human mRNA samples were implementd following standard Agilent protocol.

2011-09-25 | E-GEOD-32371 | biostudies-arrayexpress

The dynamics of DNA methylation fidelity during mouse embryonic stem cell renewal and differentiation

Project description:Purpose: we aimed to gain a genome-wide view of the dynamics in DNA methylation inheritance and define the factors associated with methylation fidelity. Methods: Using mouse embryonic stem cell (ES-E14TG2a) in both undifferentiated and differentiated states as a model system, we exploited the hairpin bisulfite sequencing approach to generate methylation data for DNA double strands simultaneously at single-base resolution. We generated the genome-wide hairpin bisulfite sequencing data to capture the methylation pattern variation during the stem cell transition from self-renewal to commitment, and integrated with various M-bM-^@M-^\omicsM-bM-^@M-^] data to scrutinize the relationships among DNA methylation inheritance, gene expression, histone modification, transcriptional factor binding and distribution of 5-hydroxylmethylation cytosine. Results and conclusion: Our results indicated that DNA methylation fidelity increases globally during early mouse embryonic stem cell differentiation. Methylation fidelity is remarkably high in promoter regions of actively expressed genes and positively correlated with active histone modification marks and binding of transcriptional factors. Strikingly, methylation fidelity follows a bimodal distribution for the intermediately methylated CpG dyads. In addition, the methylation difference in between two DNA strands rather than different DNA molecules is a major source of the intermediate DNA methylation. Lastly, while 5-hmC and 5-mC tend to coexist, no significant increase in the pairing with unmethylated cytosine was observed. For mouse embryonic stem cell of undifferentiated and spontaneous differentiated states, we determined DNA double strands methylation pattern by hairpin bisulfite sequencing approach and determined gene expression profiles using RNA-seq.

2014-05-12 | E-GEOD-48229 | biostudies-arrayexpress

The dynamics of DNA methylation fidelity during mouse embryonic stem cell renewal and differentiation

Project description:Purpose: we aimed to gain a genome-wide view of the dynamics in DNA methylation inheritance and define the factors associated with methylation fidelity. Methods: Using mouse embryonic stem cell (ES-E14TG2a) in both undifferentiated and differentiated states as a model system, we exploited the hairpin bisulfite sequencing approach to generate methylation data for DNA double strands simultaneously at single-base resolution. We generated the genome-wide hairpin bisulfite sequencing data to capture the methylation pattern variation during the stem cell transition from self-renewal to commitment, and integrated with various “omics” data to scrutinize the relationships among DNA methylation inheritance, gene expression, histone modification, transcriptional factor binding and distribution of 5-hydroxylmethylation cytosine. Results and conclusion: Our results indicated that DNA methylation fidelity increases globally during early mouse embryonic stem cell differentiation. Methylation fidelity is remarkably high in promoter regions of actively expressed genes and positively correlated with active histone modification marks and binding of transcriptional factors. Strikingly, methylation fidelity follows a bimodal distribution for the intermediately methylated CpG dyads. In addition, the methylation difference in between two DNA strands rather than different DNA molecules is a major source of the intermediate DNA methylation. Lastly, while 5-hmC and 5-mC tend to coexist, no significant increase in the pairing with unmethylated cytosine was observed.

2014-05-12 | GSE48229 | GEO

Arginine methylation of METTL14 promotes RNA N6-methyladenosine modification and endoderm differentiation of mouse embryonic stem cells

Project description:m6A is the most abundant modification of mRNA in mammals and plays an important role in human development and disease. METTL14 is a key component of m6A methyltransferase complex. The project showed that its post-translational arginine methylation can regulate the generation of m6A and the endoderm differentiation of mouse embryonic stem cells, indicating its essential function in the normal development of embryos.

2021-05-17 | PXD018458 | iProX

DNA methylation patterns expose variations in enhancer-chromatin modifications during embryonic stem cell differentiation.