Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reduced Representational Bisulfite Sequencing of R1 and Dnmt1 Tet/Tet mouse embryonic stem cell lines

ABSTRACT: We generated RRBS data to enable a comparative DNA methylation analysis of Dnmt1 Tet/Tet, a mouse embyonic stem cell line (ESC) that overexpresses DNMT1 and the WT R1 ESCs and their neuronal derivatives. The optimized data analysis workflows provides a framework for comparative investigations of methylation profiles. This platform offers a comprehensive and more accurate quantitative and qualitative evaluation of methylated cytosines in ESCs and neurons. We expect that RRBS-based methylome analysis permits to understand the epigenetic basis of abnormal neurogenesis.

ORGANISM(S): Mus musculus

PROVIDER: GSE152817 | GEO | 2020/09/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Reduced Representational Bisulfite Sequencing of R1 and Dnmt1 Tet/Tet mouse embryonic stem cell lines

Project description:Reduced Representational Bisulfite Sequencing of R1 and Dnmt1 Tet/Tet mouse embryonic stem cell lines

| PRJNA640537 | ENA

DNMT1 Tet EScells

Project description:DNMT1 TET EScells Imprinted like

| PRJEB6698 | ENA

Project description:Study of the transcriptome profiles of R1 and Dnmt1 Tet/Tet ESCs and their neuronal derivatives

| PRJNA941810 | ENA

Tet

Project description:Drosophila melanogaster Tet, Ten-Eleven Translocation (TET) family protein, is expressed in 4 baseline experiment(s);

| FBgn0263392 | ExpressionAtlas

Tet

Project description:Drosophila melanogaster Tet, Ten-Eleven Translocation (TET) family protein, is differentially expressed in 11 experiment(s);

| FBgn0263392 | ExpressionAtlas

scRNAseq studies of pMHCII-NP-induced Tet+ cells with different insulin-epitopes

Project description:SMARTseq2 scRNAseq analysis was performed on Tet+ and Tet- (Tconv) induced with 3 different insulin epitopes specificities (InsB12-20-CT-R1/IAg7, InsB13-21-R2/IAg7 and InsB10-23-CT_R3/IAg7) to study transcriptional reprogramming to different registers of the same epitope

2023-03-31 | GSE173824 | GEO

Tet proteins in DNA demethylation and cell fate restriction

Project description:DNA methylation at 5-position of cytosine (5mC) is one of the best studied epigenetic modifications that plays important roles in diverse biological processes. Iterative oxidation of 5mC by the Ten-eleven translocation (Tet) family of proteins generates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), which can be further processed by DNA repair proteins leading to DNA demethylation. Functional characterization of the Tet proteins has been complicated by the redundancy between the three Tet proteins. Using the CRISPR/Cas9 technology, we have generated mouse embryonic stem cells (ESCs) deficient for all three Tet proteins (TKO). Whole genome bisulphite sequencing (WGBS) analysis revealed that Tet-mediated DNA demethylation mainly occurs distal enhancers as well as promoters that significantly overlap with 5hmC, 5fC and 5caC. Characterization of the Tet TKO ESCs revealed a function for Tet proteins in cell fate restriction as Tet TKO ESCs tend to adopt both primed pluripotent stem cell-like state and 2-cell embryo-like state. In addition, Tet TKO ESCs exhibit elongated telomeres. Thus, our study reveals a role of Tet proteins not only in DNA demethylation, but also in cell fate restriction and telomere maintenance. 2 samples for WGBS and 2 samples for RNA-seq

2014-09-22 | E-GEOD-56986 | biostudies-arrayexpress

Tet proteins in DNA demethylation and cell fate restriction

2014-09-22 | GSE56986 | GEO

RNA-Seq profiling of mESCs and their neuronal derivatives overexpressing WT DNMT1 and DNMT1Y495C mutant form

Project description:To understand the molecular basis of neurodevelopmental abnormalities in HSAN1E disorder associated with DNMT1 Y495C mutation, we have developed transgenic mouse ES lines (R1Dnmt1 Y495C) that expresses mutant transcripts in addition to the endogenous wild-type transcripts. We also generated a transgenic cell line that overexpresses the wild-type transcripts (R1wt Dnmt1) to segregate the effects of mutant proteins. We performed transcriptome profiling of mESC lines and their neuronal derivatives using RNA-seq. Dysregulated transcripts in R1wt Dnmt1 and R1Dnmt1 Y495C mESCs and neurons were identified by comparisons with the wild-type counterpart (R1; wild-type mESC line). Gene ontology and pathway enrichment analysis were performed to identify potential pathways and key regulatory genes underlying the HSAN1E associated neurodevelopmental phenotypes.

2023-12-01 | E-MTAB-13337 | biostudies-arrayexpress

R1 ESC

Project description:R1

2011-05-07 | GSE29102 | GEO