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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
GenomicsSequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here we present sequential ChIP-bisulfite-sequencing (ChIP- BS-seq) as an approach to quantitatively ...
ORGANISM(S): Homo sapiens 
2012-03-27 | E-GEOD-28254 | biostudies-arrayexpress
GenomicsA Probabilistic Model of Transcription Dynamics applied to Estrogen Signalling in Breast Cancer Cells
Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influences the rate and timing of gene expression. In this work we present a probabilistic model of transcription dynamics which is f...
ORGANISM(S): Homo sapiens 
2014-05-19 | E-GEOD-44800 | biostudies-arrayexpress
GenomicsChIP-Seq sequencing of novel interactors of H3K4me3, H3K36me3 and H3K9me3
This study describes the epigenetic profiling of the novel interactors of H3K4me3, H3K36me3 or H3K9me3. The interactors were ChIP-Seq profiled by their GFP tag in stably transfected HeLa (Kyoto) cells. The interactors include GATAD1, Sgf29, BAP18, TRRAP, PHF8, N-PAC and LRWD1 (including replicates),...
ORGANISM(S): Homo sapiens 
2010-09-17 | E-GEOD-20303 | biostudies-arrayexpress
GenomicsGenome wide profiling of MBD2 binding
We show that in vivo MBD2 is mainly recruited to CpG island promoters that are highly methylated. We also report that MBD2 binds to a subset of CpG island promoters that are characterized by the presence of active histone marks and RNA polymerase II (Pol2). At such sites, MBD2 binds downstream of th...
ORGANISM(S): Homo sapiens 
2014-07-03 | E-GEOD-54693 | biostudies-arrayexpress
GenomicsComparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions in 24 tumor and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hypomethylated regions were identified, which include potent...
ORGANISM(S): Homo sapiens 
2012-10-26 | E-GEOD-39068 | biostudies-arrayexpress
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