Genomics

Dataset Information

91

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq)


ABSTRACT: 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 allowed us to identify locations of individual transcription factor binding sites that protected against the bound DNA against digestion. To measure the accuracy of these footprints, we also generated ChIP-seq data for the CTCF DNA binding factor in the same cell growths. We found that DNaseI footprints containing the CTCF canonical binding motif show significant ChIP-seq signal while CTCF binding motifs not in footprints show almost no signal providing one measure of valdation of the DNaseI footprints. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Five cell lines representing cervica carcinoma, chronic myeloid leukemia, embryonic stem cells, epidermal keratinocytes, and umbilical vein endothelial cells were analyzed using ChIP-seq.

ORGANISM(S): Homo sapiens  

SUBMITTER: Gregory E Crawford  Vishwanath R Iyer   Terrence S Furey   Terry Furey    

PROVIDER: E-GEOD-25416 | ArrayExpress| 2014-05-02

SECONDARY ACCESSION(S): SRP004455GSE25416

REPOSITORIES: GEO, ArrayExpress, ENA

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High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Boyle Alan P AP   Song Lingyun L   Lee Bum-Kyu BK   London Darin D   Keefe Damian D   Birney Ewan E   Iyer Vishwanath R VR   Crawford Gregory E GE   Furey Terrence S TS  

Genome research 20101124 3


Regulation of gene transcription in diverse cell types is determined largely by varied sets of cis-elements where transcription factors bind. Here we demonstrate that data from a single high-throughput DNase I hypersensitivity assay can delineate hundreds of thousands of base-pair resolution in vivo footprints in human cells that precisely mark individual transcription factor-DNA interactions. These annotations provide a unique resource for the investigation of cis-regulatory elements. We find t  ...[more]

Publication: 1/2

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