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GenomicsG-Quadruplex structures are stable and detectable in human genomic DNA.
The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is ...
ORGANISM(S): Homo sapiens 
2013-05-08 | E-GEOD-45241 | biostudies-arrayexpress
GenomicsGenome-wide distribution of 5-formylcytosine in ES cells is associated with transcription and depends on TDG
Methylation of cytosine in DNA (5mC) is an important epigenetic mark that is involved in the regulation of genome function. During early embryonic development in mammals, the DNA methylation landscape is dynamically reprogrammed in part through active demethylation. Recent advances have identified k...
ORGANISM(S): Mus musculus 
2012-08-17 | E-GEOD-40148 | biostudies-arrayexpress
GenomicsGenome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor alpha in breast cancer cells
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Homo sapiens 
2013-01-07 | E-GEOD-40767 | biostudies-arrayexpress
GenomicsEnhanced methylome sequencing by recovery of unsequenceable fragments
Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemistry renders the majority of DNA fragments unsequenceable, thus necessitating PCR amplification. Furthermore, bisulfite conversion generates an A...
ORGANISM(S): Plasmodium berghei ANKA 
2016-03-16 | E-GEOD-65116 | biostudies-arrayexpress
TranscriptomicsGenome-wide mapping of FOXM1 binding reveals co-binding with oestrogen receptor alpha in breast cancer cells (expression)
The forkhead transcription factor FOXM1 is a key regulator of the cell cycle and is overexpressed in cancer. Increased levels of FOXM1 are associated with both poor prognosis and oestrogen receptor (ERalpha) status in primary breast cancer. In this study, we map FOXM1 binding genome wide in both ERa...
ORGANISM(S): Homo sapiens 
2013-01-07 | E-GEOD-40766 | biostudies-arrayexpress
GenomicsGenome-wide mapping of FOXM1 binding reveals co-binding with oestrogen receptor alpha in breast cancer cells (ChIP-seq)
The forkhead transcription factor FOXM1 is a key regulator of the cell cycle and is overexpressed in cancer. Increased levels of FOXM1 are associated with both poor prognosis and oestrogen receptor (ERalpha) status in primary breast cancer. In this study, we map FOXM1 binding genome wide in both ERa...
ORGANISM(S): Homo sapiens 
2013-01-07 | E-GEOD-40762 | biostudies-arrayexpress
GenomicsQuantitative sequencing of 5-formylcytosine in DNA at single-base resolution
Cytosine base modifications 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) are present in mammalian DNA. Here, reduced bisulfite sequencing is developed for quantitatively sequencing 5fC at single-base resolution. This method is then applied with oxidative bisulfit...
ORGANISM(S): Mus musculus 
2014-04-08 | E-GEOD-56572 | biostudies-arrayexpress
TranscriptomicsExpression data from pig BMDM treated with salmonella LPS
Mouse bone marrow-derived macrophages (BMDM) grown in macrophage colony-stimulating factor (CSF-1) have been used widely in studies of macrophage biology and the response to toll-like receptor agonists. We investigated whether similar cells could be derived from the domestic pig. Cultivation of pig ...
ORGANISM(S): Sus scrofa 
2011-08-31 | E-GEOD-30956 | biostudies-arrayexpress
TranscriptomicsG-quadruplex structures mark human regulatory chromatin
DNA secondary structures are important for fundamental genome functions such as transcription and replication1. The G-quadruplex (G4) structural motif has been linked to gene regulation2,3 and genome instability4,5 and may be important to cancer development and other diseases6-8. Recently, ~700,000 ...
ORGANISM(S): Homo sapiens 
2016-08-05 | E-GEOD-76688 | biostudies-arrayexpress
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