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GenomicsCTCF demarcates chromatin domains
Insulators are DNA elements, which prevent inappropriate interactions between the neighboring regions of the genome. They can be functionally classified as either enhancer blockers or domain barriers. CTCF (CCCTC binding factor) is the only known major insulator binding protein in the vertebrates a...
ORGANISM(S): Homo sapiens 
2008-10-20 | E-GEOD-12889 | biostudies-arrayexpress
GenomicsCTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [ChIP-Seq]
The goal of this study was to investigate the role of intragenic CTCF in alternative pre-mRNA splicing through a combined CTCF-ChIP-seq and RNA-seq approach. CTCF depletion led to decreased inclusion of weak upstream exons. CTCF ChIP-seq was performed in BJAB and BL41 B cell lines and normalized rel...
ORGANISM(S): Homo sapiens 
2011-10-06 | E-GEOD-31485 | biostudies-arrayexpress
GenomicsChIP-seq analysis of CTCF binding sites in lymphocyte subsets [DN thymocytes]
In this study, we compare the binding pattern of CTCF at the T cell receptor alpha locus in different subsets of developing lymphocytes. For the ChIP-seq, input and immunoprecipitated DNA was given to The Scripps DNA Array Facility, where it was prepared for massively parallel sequencing on Illumin...
ORGANISM(S): Mus musculus 
2012-12-03 | E-GEOD-41739 | biostudies-arrayexpress
GenomicsChIP-seq analysis of CTCF binding sites in lymphocyte subsets [DP thymocytes]
In this study, we compare the binding pattern of CTCF at the T cell receptor alpha locus in different subsets of developing lymphocytes For the ChIP-seq, input and immunoprecipitated DNA was given to The Scripps DNA Array Facility, where it was prepared for massively parallel sequencing on Illumina...
ORGANISM(S): Mus musculus 
2012-12-03 | E-GEOD-41740 | biostudies-arrayexpress
GenomicsChIP-seq analysis of CTCF binding sites in lymphocyte subsets [pro-B cells]
In this study, we compare the binding pattern of CTCF at the T cell receptor alpha locus in different subsets of developing lymphocytes For the ChIP-seq, input and immunoprecipitated DNA was given to The Scripps DNA Array Facility, where it was prepared for massively parallel sequencing on Illumina...
ORGANISM(S): Mus musculus 
2012-12-03 | E-GEOD-41741 | biostudies-arrayexpress
TranscriptomicsCTCF binding polarity determines chromatin looping [4C]
CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional organization of chromatin. In this study, we systematically assayed the 3D genomic contact profiles of hundreds of CTCF binding sites in multiple tissues with high-resolution 4C-seq. We find both developmentall...
ORGANISM(S): Mus musculus 
2015-10-29 | E-GEOD-72539 | biostudies-arrayexpress
GenomicsX-chromosome dynamics revealed by the RNA interactome and chromosomal binding of CTCF
CTCF is a master regulator that plays a role in genome architecture and gene expression. A key aspect of CTCF’s mechanism involves bringing together distant genetic elements for intra- and inter-chromosomal interactions. Evidence from epigenetic processes, such as X-chromosome inactivation (XCI), su...
ORGANISM(S): Mus musculus 
2015-01-09 | E-GEOD-58242 | biostudies-arrayexpress
TranscriptomicsCTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [RNA-Seq]
The goal of this study was to investigate the role of intragenic CTCF in alternative pre-mRNA splicing through a combined CTCF-ChIP-seq and RNA-seq approach. CTCF depletion led to decreased inclusion of weak upstream exons. CTCF ChIP-seq was performed in BJAB and BL41 B cell lines and normalized rel...
ORGANISM(S): Homo sapiens 
2011-10-06 | E-GEOD-31486 | biostudies-arrayexpress
GenomicsNucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF
This SuperSeries is composed of the following subset Series: GSE34091: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [Mouse430_2 Expression] GSE34092: Nucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTC...
ORGANISM(S): Mus musculus 
2012-07-24 | E-GEOD-34093 | biostudies-arrayexpress
GenomicsNucleosome dynamics specifies genome-wide binding of the male germ cell gene regulator CTCFL and of CTCF [ChIP-Seq]
CTCF and CTCFL DNA binding profile in CTCFL induced and non-induced ES cells.CTCF is a highly conserved and essential zinc finger protein that in conjunction with cohesin organizes chromatin into loops, thereby regulating gene expression and epigenetic events. The function of CTCFL or BORIS, the tes...
ORGANISM(S): Mus musculus 
2012-07-25 | E-GEOD-34094 | biostudies-arrayexpress
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