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GenomicsMeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system
The high level of 5-hydroxymethylcytosine (5hmC) present in neuronal genomes suggests that mechanisms interpreting 5hmC in the central nervous system (CNS) may differ from those present in embryonic stem cells. Here we present quantitative, genome-wide analysis of 5hmC, 5- methylcytosine (5mC) an...
ORGANISM(S): Mus musculus 
2013-01-14 | E-GEOD-42880 | biostudies-arrayexpress
TranscriptomicsApplication of a low cost array-based technique - TAB-Array - for quantifying and mapping both 5mC and 5hmC at single base resolution.
5-hydroxymethylcytosine (5hmC), an oxidized derivative of 5-methylcytosine (5mC), has been implicated as an important epigenetic regulator of mammalian development. Current procedures use cost-prohibitive DNA sequencing methods to discriminate 5hmC from 5mC, limiting their accessibility to the scie...
ORGANISM(S): Homo sapiens 
2014-12-12 | E-GEOD-60225 | biostudies-arrayexpress
TranscriptomicsGenome-wide Regulation of 5hmC, 5mC and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells (ChIP-seq data)
DNA methylation of C5-cytosine (5mC) in the mammalian genome is a key epigenetic event that is critical for various cellular processes. However, how the genome-wide 5mC pattern is dynamically regulated remains a fundamental question in epigenetic biology. The TET family of 5mC hydroxylases, which co...
ORGANISM(S): Mus musculus 
2011-04-21 | E-GEOD-28532 | 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
TranscriptomicsGenome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells
Recent studies have demonstrated that the Ten-eleven translocation (Tet) family proteins can enzymatically convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While 5mC has been studied extensively, little is known about the distribution and function of 5hmC. Here we present a genome...
ORGANISM(S): Mus musculus 
2011-03-30 | E-GEOD-27613 | biostudies-arrayexpress
GenomicsMeDIP analysis of 5mC and 5hmC marks in human ataxia-telangiectasia cerebellum
Genomic DNA was prepared, fragmented, and immunoprecipitated with antibodies specific for 5mC or 5hmC prior to standard sequencing. The neurodegenerative disease known as ataxia-telangiectasia (A-T) is caused by the absence of the ATM (A-T mutated) protein. A long-standing mystery surrounding A-T i...
ORGANISM(S): Homo sapiens 
2015-10-30 | E-GEOD-61133 | biostudies-arrayexpress
TranscriptomicsSelective loss of 5hmC links to A-T Purkinje cell vulnerability
This SuperSeries is composed of the SubSeries listed below. The neurodegenerative disease known as ataxia-telangiectasia (A-T) is caused by the absence of the ATM (A-T mutated) protein. A long-standing mystery surrounding A-T is why cerebellar Purkinje cells (PCs) appear uniquely vulnerable to ATM-...
ORGANISM(S): Homo sapiens 
2015-10-30 | E-GEOD-61169 | biostudies-arrayexpress
GenomicsA highly sensitive and robust method for genome-wide 5hmC profiling of rare cell populations
Investigations of 5-hydroxymethylcytosine (5hmC) in biologically and clinically samples and models with low cell numbers have been hampered by the low sensitivity and reproducibility using current 5hmC mapping approaches. Here, we develop a selective 5hmC chemical labeling approach using tagmentatio...
ORGANISM(S): Mus musculus 
2016-09-01 | E-GEOD-77967 | biostudies-arrayexpress
GenomicsJBP1-seq: a fast and efficient method for genome-wide profiling of 5hmC
We developed a novel approach, J-binding protein 1 sequencing (JBP1-seq), that combines the benefits of an improved recombinant JBP1 protein, Nextera-based library construction, and nextgeneration sequencing (NGS) for genome-wide profiling of 5-hydroxymethylcytosine (5hmC). Compared with the orig...
ORGANISM(S): Homo sapiens 
2014-11-26 | E-GEOD-61193 | biostudies-arrayexpress
GenomicsPCGP Dyer_iPSC 5hmc - samples
DATA FILES FOR PCGP Dyer_iPSC 5hmc
EGAD00001001418 | EGA
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