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Transcriptomics5-hydroxymethylcytosine marks promoters in colon that resist hypermethylation in cancer [Methylation450 Array]
The discovery of cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behavior in colon cancer. 5-hmC is globally reduced in proliferating cells such as colon tumors and the gut crypt progenitors, fro...
ORGANISM(S): Homo sapiens 
2015-02-03 | E-GEOD-63421 | biostudies-arrayexpress
GenomicsSox9 controls self-renewal of oncogene targeted cells and links tumor initiation and invasion [ChIP-Seq]
Sox9 is a transcription factor expressed in most solid tumors. However, the molecular mechanisms underlying Sox9 function during tumorigenesis remain unclear. Here, using a genetic mouse model of basal cell carcinoma (BCC), the most frequent cancer in human, we show that Sox9 is expressed from the e...
ORGANISM(S): Mus musculus 
2015-05-13 | E-GEOD-68755 | biostudies-arrayexpress
TranscriptomicsEvaluation of the Infinium Methylation 450K technology
Genome-wide DNA methylation profiling of HCT116 WT, HCT116 DNMT1 and DNMT3B double KO, and breast cancer tumors by next generation Infinium assay Bisulfite converted DNA from 22 samples were hybridized to the Illumina's HumanMethylation450 BeadChip
ORGANISM(S): Homo sapiens 
2011-12-15 | E-GEOD-29290 | biostudies-arrayexpress
TranscriptomicsRegulation of DNA methylation by CK2-mediated phosphorylation of DNMT3A (Beadchip)
DNA methylation is a central epigenetic modification that has essential roles in cellular processes including chromatin structure, gene regulation, development and disease. The de novo DNA methyltransferases are responsible for the generation of genomic methylation patterns, but the underlying mecha...
ORGANISM(S): Homo sapiens 
2014-07-17 | E-GEOD-26164 | biostudies-arrayexpress
GenomicsTET2 and TET3 regulate GlcNAcylation and H3K4 methylation through OGT and SET1/COMPASS
TET proteins convert 5-methylcytosine to 5-hydroxymethylcytosine, an emerging dynamic epigenetic state of DNA that can influence transcription. Evidence has linked TET1 function to epigenetic repression complexes, yet mechanistic information, especially for the TET2 and TET3 proteins, remains limite...
ORGANISM(S): Mus musculus 
2013-02-07 | E-GEOD-36620 | biostudies-arrayexpress
GenomicsGenome-wide hydroxymethylcytosine pattern changes in response to oxidative stress
The TET-family enzymes (TETs) convert methylcytosine to hydroxymethylcytosine, a lately discovered epigenetic modification that can modulate transcription. While recent reports suggest that TETs may play a role in response to oxidative stress, this role remains uncertain. Here we show that Tet1 is s...
ORGANISM(S): Homo sapiens 
2016-01-14 | E-GEOD-59718 | biostudies-arrayexpress
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