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Series GSE25416 Query DataSets for GSE25416
Status Public on Nov 18, 2010
Title High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells (ChIP-seq)
Project ENCODE
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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 and
Overall design Five cell lines representing cervica carcinoma, chronic myeloid leukemia, embryonic stem cells, epidermal keratinocytes, and umbilical vein endothelial cells were analyzed using ChIP-seq.
Web link
Contributor(s) Iyer VR, Furey TS, Crawford GE
Citation(s) 21106903, 21750106
BioProject PRJNA63443
Submission date Nov 16, 2010
Last update date May 15, 2019
Contact name Terry Furey
Organization name UNC-Chapel Hill
Department Genetics
Lab Furey
Street address 5022 Genetic Medicine Building, CB#7264
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (5)
GSM624078 HelaS3_CHIP_CTCF
This SubSeries is part of SuperSeries:
GSE25442 High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells
GSE30227 Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
GSE32883 Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
SRA SRP004455

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE25416_RAW.tar 1.3 Gb (http)(custom) TAR (of BED, TXT)
GSE25416_README.txt 928 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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