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GenomicsWhole genome DNAse hypersensitivity in human CD4+ T-cells
Mapping DNaseI hypersensitive (HS) sites is an accurate method of identifying the location of genetic regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. We employed whole genome tiled array strategies to identify DNaseI HS sites within human prima...
ORGANISM(S): Homo sapiens 
2007-11-19 | E-GEOD-8486 | biostudies-arrayexpress
GenomicsHigh-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (Dnase-seq)
Using DNaseI hypersensitivity (HS) assays (Dnase-seq), high resolution DNaseI digestion profiles were generated genome-wide in diverse human cell types. We showed that within general regions of DNaseI HS that are known to identify locations of gene regulatory elements, DNaseI digestion patterns all...
ORGANISM(S): Homo sapiens 
2010-11-18 | E-GEOD-25344 | biostudies-arrayexpress
GenomicsOpen chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [DNase_seq].
The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of di...
ORGANISM(S): Homo sapiens 
2011-06-29 | E-GEOD-30224 | biostudies-arrayexpress
GenomicsMicrobiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape
We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota. We show that regional differences in gene transcription along the intestinal tract were accompanied by major alterations in chromatin organiz...
ORGANISM(S): Mus musculus 
2014-06-07 | E-GEOD-57919 | biostudies-arrayexpress
GenomicsCell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells [new ChIP-Seq samples]
Cellular diversity in a multicellular organism like the human is achieved in part by distinct programs of gene expression at the level of transcription, which in turn are mediated by transcription factors (TFs). However, there are few systematic studies of the genomic binding of different types of T...
ORGANISM(S): Homo sapiens 
2011-10-18 | E-GEOD-32692 | biostudies-arrayexpress
GenomicsHigh-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq)
Using DNaseI hypersensitivity (HS) assays (Dnase-seq), high resolution DNaseI digestion profiles were generated genome-wide in diverse human cell types. We showed that within general regions of DNaseI HS that are known to identify locations of gene regulatory elements, DNaseI digestion patterns all...
ORGANISM(S): Homo sapiens 
2010-11-18 | E-GEOD-25416 | biostudies-arrayexpress
GenomicsOpen chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [FAIRE_seq]
The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of di...
ORGANISM(S): Homo sapiens 
2011-06-29 | E-GEOD-30225 | biostudies-arrayexpress
GenomicsOpen chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [ChIP_seq].
The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of di...
ORGANISM(S): Homo sapiens 
2011-06-29 | E-GEOD-30226 | biostudies-arrayexpress
GenomicsDNase I hypersensitive sites in two tissues of rice
Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide ...
ORGANISM(S): Oryza sativa 
2011-11-09 | E-GEOD-26610 | biostudies-arrayexpress
TranscriptomicsGenome-Wide Specificity of DNA-Binding, Gene Regulation, and Chromatin Remodeling by TALE- and CRISPR/Cas9-Based Transcription Factors
Synthetic DNA-binding proteins have found broad application in gene therapies and as tools for interrogating biology. Engineered proteins based on the CRISPR/Cas9 and TALE systems have been used to alter genomic DNA sequences, control transcription of endogenous genes, and modify epigenetic states. ...
ORGANISM(S): Homo sapiens 
2015-05-27 | E-GEOD-68341 | biostudies-arrayexpress
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