|
| 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 http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| |
|
| 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 |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
|
| |
|
| 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 |
| E-mail(s) |
terry.furey@unc.edu
|
| 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)
|
|
| 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 |
|
| Relations |
| SRA |
SRP004455 |
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