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TranscriptomicsChromatin immunoprecipitation of human cell lines to identify cAMP-response element binding protein (CREB) binding sites.
Hormones and nutrients often induce genetic programs via signaling pathways that interface with gene-specific activators. Activation of the cAMP pathway, for example, stimulates cellular gene expression by means of the PKA-mediated phosphorylation of cAMP-response element binding protein (CREB) at S...
ORGANISM(S): Homo sapiens 
2006-05-09 | E-WMIT-11 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation genome wide map of nucleosome acetylation and methylation in Yeast
Genomes are packaged into nucleosomes whose position and modification state can profoundly influence regulation of gene expression. We have established new ChIP-based high-resolution genome-wide maps of histone acetylation and methylation that take into account changes in nucleosome occupancy at act...
ORGANISM(S): Saccharomyces cerevisiae 
2005-08-25 | E-WMIT-3 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of human HNF3b and E2F4, and mouse NeuroD1, for THEME analysis
Genome-wide chromatin-immunoprecipitation (ChIP-chip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover sequence patterns in the bound regions that may be recognized by the immunoprecipitated protein. However, the disco...
ORGANISM(S): Mus musculus 
2006-05-09 | E-WMIT-8 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of Foxp3 in mouse T-cell hybridoma cells
The forkhead transcription factor Foxp3 is essential for the development of CD4+CD25+ regulatory T (Treg) cells and prevention of autoimmunity, but how it controls the Treg gene expression program is not understood. We describe here genome-wide location and expression data that identify Foxp3 targe...
ORGANISM(S): Mus musculus 
2007-01-27 | E-TABM-154 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of human MLL1 to understand its role in cell type specification
An experiment was performed to understand its role in cell type specification, we have determined the human genomic binding sites of MLL1. MLL1 localizes with Pol II to the 5' end of actively transcribed genes, where histone H3 lysine 4 (H3-K4) trimethylation occurs. The ability of MLL1 to serve as ...
ORGANISM(S): Homo sapiens 
2005-06-03 | E-WMIT-4 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of Tcf3, Oct4 and nanog in mouse embryonic stem cells
Embryonic stem cells have a unique regulatory circuitry, largely controlled by the transcription factors Oct4, Sox2 and Nanog, which generates a gene expression program necessary for pluripotency and self-renewal (Boyer et al. 2005; Loh et al. 2006; Chambers et al. 2003; Mitsui et al. 2003; Nichols ...
ORGANISM(S): Mus musculus 
2008-02-28 | E-TABM-409 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation analysis of human hepatocyte regulatory circuitry
We mapped the transcriptional regulatory circuitry for six master regulators in human hepatocytes using chromatin immunoprecipitation and high-resolution promoter microarrays. The results show that these regulators form a highly interconnected core circuitry, and reveal the local regulatory network ...
ORGANISM(S): Homo sapiens 
2006-05-09 | E-WMIT-9 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of human cells after lipopolysaccharide stimulation, to identify binding of NF-KappaB family members
The NF-KappaB family of transcription factors plays a critical role in numerous cellular processes, particularly the immune response. Our understanding of how the different NF-kappaB subunits act coordinately to regulate gene expression is based on a limited set of genes. We used genome-scale locati...
ORGANISM(S): Homo sapiens 
2006-05-09 | E-WMIT-6 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of Drosophila embryos to investigate RNA polymerase stalling at developmental control genes
Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determine the genome-wide occupancy of the dorsoventral determinants Dorsal, Twist and Snail in the Drosophila emb...
ORGANISM(S): Drosophila melanogaster 
2007-11-15 | E-TABM-322 | biostudies-arrayexpress
TranscriptomicsChromatin immunoprecipitation of the dorsoventral determinants Dorsal, Twist and Snail in the Drosophila embryo
Genetic studies have identified numerous sequence-specific transcription factors that control development, yet little is known about their in vivo distribution across animal genomes. We determine the genome-wide occupancy of the dorsoventral determinants Dorsal, Twist and Snail in the Drosophila emb...
ORGANISM(S): Drosophila melanogaster 
2007-08-31 | E-TABM-226 | biostudies-arrayexpress
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