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TranscriptomicsDeep Sequence Analysis of the Relationship between Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells
We used deep sequencinge technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cance...
ORGANISM(S): Homo sapiens 
2011-03-16 | E-GEOD-27003 | biostudies-arrayexpress
TranscriptomicsCpG islands recruit a histone H3 lysine 36 demethylase [Agilent data]
Transcription factors that bind small DNA motifs embedded in promoters play a central role in controlling gene expression. However, in addition to these elements, up to 70% of genes in higher eukaryotes also have high levels of non-methylated cytosine/guanine base pairs (CpGs) surrounding promoters ...
ORGANISM(S): Homo sapiens 
2010-05-27 | E-GEOD-21201 | biostudies-arrayexpress
TranscriptomicsClustering of CpG islands constitutes an important determinant of the interphase chromosome 3D organization [4C-Seq]
Using 4C-Seq experimental procedure we have characterized, in cultured chicken lymphoid and erythroid cells, genome-wide patterns of spatial contacts of several CpG islands scattered along the chromosome 14. A clear tendency for interaction of CpG islands present within the same and different chromo...
ORGANISM(S): Gallus gallus 
2014-03-01 | E-GEOD-51937 | biostudies-arrayexpress
GenomicsCpG islands recruit a histone H3 lysine 36 demethylase
This SuperSeries is composed of the following subset Series: GSE18588: CpG islands recruit a histone H3 lysine 36 demethylase [Illumina sequencing data] GSE21201: CpG islands recruit a histone H3 lysine 36 demethylase [Agilent data] Refer to individual Series
ORGANISM(S): Homo sapiens 
2010-04-26 | E-GEOD-21202 | biostudies-arrayexpress
GenomicsCpG islands recruit a histone H3 lysine 36 demethylase [Illumina sequencing data]
Eukaryotic gene expression profiles are largely defined by transcription factors that recognize specific DNA sequences in gene regulatory regions and impact RNA polymerase recruitment and transcription. In addition to specific core promoter regulatory elements, up to 70% of genes in higher eukaryote...
ORGANISM(S): Mus musculus 
2010-04-27 | E-GEOD-18588 | biostudies-arrayexpress
TranscriptomicsIsocitrate dehydrogenase 1 (IDH1) mutant gliomas demonstrate a distinct global CpG island methylation profile compared to IDH1 wildtype gliomas using MRSE
In order to identify other molecular aberrations that may cooperate with IDH1R132MUT in gliomagenesis, we performed CpG-island methylation profiling analysis using MSRE (Tran et al. Front. Neurosci. 3:57. Doi: 10.3389/neuro.15.005.2009) on a subset of IDH1R132MUT and IDH1R132WT GBMs and found a dist...
ORGANISM(S): Homo sapiens 
2011-10-24 | E-GEOD-28271 | biostudies-arrayexpress
GenomicsKDM2B binds CpG islands and modulates recruitment of Ring1b
CpG island elements are associated with most mammalian gene promoters, yet how they contribute to gene regulation remains poorly understood. Recently it has become clear that a subset of CpG islands in embryonic stem cells can act as polycomb response elements and are recognized by the polycomb sile...
ORGANISM(S): Mus musculus 
2012-12-26 | E-GEOD-40860 | biostudies-arrayexpress
TranscriptomicsMethylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 1
Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. W...
ORGANISM(S): Homo sapiens 
2009-04-28 | E-GEOD-15746 | biostudies-arrayexpress
TranscriptomicsGENOME-WIDE CpG ISLAND METHYLATION ANALYSIS IN NON-SMALL CELL LUNG CANCER PATIENTS [Affymetrix expression data]
Epigenetic changes largely contribute to the regulation of gene expression in cancer cells. DNA methylation is part of the epigenetic gene regulation complex which is relevant for the pathogenesis of cancer. We performed a genome-wide search for methylated CpG islands in tumors and corresponding non...
ORGANISM(S): Homo sapiens 
2012-11-26 | E-GEOD-32496 | biostudies-arrayexpress
TranscriptomicsThe presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands.
Instructive mechanisms are present for induction of DNA methylation, as shown by methylation of specific CpG islands (CGIs) by specific inducers and in specific cancers. However, instructive factors involved are poorly understood, except for involvement of low transcription and trimethylation of his...
ORGANISM(S): Homo sapiens 
2010-05-15 | E-GEOD-15154 | biostudies-arrayexpress
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