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| Status |
Public on Jun 12, 2015 |
| Title |
A simple method for generating high-resolution maps of genome wide protein binding |
| Organisms |
Drosophila melanogaster; Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution and newer techniques require significant experimental alterations and complex bioinformatics. Here we build upon our high-resolution crosslinking ChIP-seq (X-ChIP-seq) method and compare it to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity to fragment the chromatin and thereby generate precise protein-DNA footprints, high-resolution X-ChIP-seq achieves single base pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing.
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| Overall design |
Using High-resolution X-ChIP-seq we determined the genome-wide binding profile of various DNA binding proteins.
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| Contributor(s) |
Skene PJ, Henikoff S |
| Citation(s) |
26079792 |
| Submission date |
Mar 31, 2015 |
| Last update date |
Jul 13, 2020 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
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| Platforms (3) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA279984 |
| SRA |
SRP056749 |
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