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GenomicsDissecting the dynamic changes of 5-hydroxymethylcytosine in T cell development and differentiation [MeDIP-Seq]
The discovery of TET proteins, enzymes that oxidize 5-methylcytosine (5mC) in DNA, has revealed novel mechanisms for the regulation of DNA methylation. We have mapped 5-hydroxymethylcytosine (5hmC) at different stages of T cell development in the thymus and T cell differentiation in the periphery. ...
ORGANISM(S): Mus musculus 
2014-08-04 | E-GEOD-59122 | biostudies-arrayexpress
GenomicsThe alteration of 5-hydroxymethylcytosine modification contributes to ischemic brain injury [5hmC-seq]
Epigenetic modifications, such as cytosine methylation and histone modification, have been shown involved in the pathology of ischemic brain injury. Recent works have implicated 5-hydroxymethylcytosine (5hmC), a DNA base derived from 5-methylcytosine (5mC) through the oxidation by Ten-Eleven Translo...
ORGANISM(S): Mus musculus 
2015-09-08 | E-GEOD-67188 | biostudies-arrayexpress
TranscriptomicsAcute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity
This SuperSeries is composed of the following subset Series: GSE34886: Acute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [expression profiling] GSE34887: Acute depletion of Tet1-dependent 5-hydroxymethylcy...
ORGANISM(S): Mus musculus 
2012-01-04 | E-GEOD-34267 | biostudies-arrayexpress
GenomicsSubsets of visceral adipose tissue nuclei with discrete levels of 5-hydroxymethylcytosine
We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We devel...
ORGANISM(S): Sus scrofa 
2016-07-20 | E-GEOD-73684 | biostudies-arrayexpress
GenomicsRRHP : a tag-based approach for 5-hydroxymethylcytosine mapping at single-site resolution
We present here a novel approach called Reduced Representation 5-Hydroxymethylcytosine Profiling (RRHP), which exploits ?-glucosyltransferase (?-GT) to inhibit restriction digestion at adapters ligated to a genomic library, such that only fragments presenting glucosylated 5hmC residues at adapter ju...
ORGANISM(S): Homo sapiens 
2014-08-26 | E-GEOD-49546 | biostudies-arrayexpress
GenomicsAcute depletion of Tet1-dependent 5-hydroxymethylcytosine levels impairs LIF/Stat3 signaling and results in loss of embryonic stem cell identity [MRE-seq]
The TET family of FE(II) and 2-oxoglutarate-dependent enzymes (Tet1/2/3) promote DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which they further oxidize into 5-formylcytosine and 5-carboxylcytosine. Tet1 is robustly expressed in mouse embryonic stem cells (mESC...
ORGANISM(S): Mus musculus 
2012-01-06 | E-GEOD-34887 | biostudies-arrayexpress
TranscriptomicsTET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer
5-hydroxymethylcytosine (5-mC) and gene expression profiling of T84 cell differentiation; 5-hmC profiling of colon cancer colonocyte fractions T84 cell differentiation was monitored as cells formed confluent monolayers in tissue culture
ORGANISM(S): Homo sapiens 
2015-12-09 | E-GEOD-69333 | biostudies-arrayexpress
Genomics5-hydroxymethylcytosine: the sixth DNA base
We performed a meta analysis of publicly available TET1, 5mC, 5hmC and genome wide bisulfite profiling data mostly from mouse embryonic stem cells (ESC). Genome wide chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) has revealed binding of the TET1 protein at CpG-island (CGI) pr...
ORGANISM(S): Mus musculus 
2011-11-24 | E-GEOD-31343 | biostudies-arrayexpress
GenomicsA key role for Mbd3 in 5-hydroxymethylcytosine-dependent gene regulation in embryonic stem cells
Numerous chromatin regulators are required for embryonic stem (ES) cell self-renewal and pluripotency, but few have been studied in detail. Here, we examine the roles of several chromatin regulators whose loss affects the pluripotent state of ES cells. We find that Mbd3 and Brg1 antagonistically reg...
ORGANISM(S): Mus musculus 
2011-12-01 | E-GEOD-31690 | biostudies-arrayexpress
ProteomicsModified cytosine binding proteins
DNA methylation (5mC) plays important roles in epigenetic regulation of genome function, and recently the TET1-3 hydroxylases have been found to oxidize 5mC to hydroxymethylcytosine (5hmC), formylcytosine (5fC), and carboxylcytosine (5caC) in DNA. These derivatives have a role in demethylation of DN...
ORGANISM(S): Mus musculus (Mouse) 
2013-10-21 | PXD000524 | Pride
Formylcytosine Pax6 Methylcytosine Hydroxymethylcytosine Es cells Fgf15 
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