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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
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
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
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
GenomicsLoss of 5-hydroxymethylcytosine is an epigenetic hallmark of melanoma
DNA methylation at the 5-position of cytosine (5-mC) is a key epigenetic mark critical for varius biological and pathological processes. 5-mC can be converted to 5-hydroxymethylcytosine (5-hmC) by the Ten-Eleven Translocation (TET) family of DNA hydroxylases. Here we report that "loss of 5-hmC&...
ORGANISM(S): Homo sapiens 
2012-09-18 | E-GEOD-38231 | 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
GenomicsSelective chemical labeling reveals intragenic enrichment of 5-hydroxymethylcytosine in mouse cerebellum
5-Methylcytosine (5-mC) is an important DNA modification found in eukaryotes that impacts gene regulation and disease pathogenesis. Recently, 5-hydroxymethylcytosine (5-hmC), another form of DNA modification, has been identified in substantial amounts in certain mammalian cell types; however, its ro...
ORGANISM(S): Mus musculus 
2010-12-12 | E-GEOD-25398 | 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
TranscriptomicsGenomic mapping of 5-hydroxymethylcytosine in the human brain
Methylation at the 5-position of cytosine is a well-studied epigenetic pathway. In addition to 5-methylcytosine (5mC), substantial amounts of 5-hydroxymethylcytosine (5hmC) also referred to as the 6th DNA base, have been detected in certain tissues, most notably the brain. However, the genomic distr...
ORGANISM(S): Homo sapiens 
2011-03-01 | E-GEOD-27051 | biostudies-arrayexpress
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