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| Status |
Public on May 25, 2016 |
| Title |
The DNA affinity purification DAP-Seq assay [ChIP-seq] |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
As 5-15% of higher eukaryotes genes are transcription factors (TFs), the lack of transcription factor binding site (TFBS) information for most factors in most organisms limits the study of gene regulation. Here we describe a next-generation sequencing method, DNA affinity purification (DAP-Seq), an in vitro gDNA/TF interaction assay that produces whole-genome TFBS annotation for any factor from any organism. Like ChIP-Seq, DAP-Seq resolves TFBS as discrete peaks at genomic locations which allows for accurate motif prediction direct assignment of functionally relevant target genes, and shows better overlap with ChIP-Seq peaks than indirect motif assignment approaches. We applied DAP-Seq to a set of 50 transcription factors in eight Arabidopsis thaliana and one Zea Mays families to gain novel biological insight into TFBS architectures, functions, evolution and methylation-sensitivity. Overall, DAP-Seq offers a low-cost high-throughput approach to identify TFBS in native sequence context for any organism complete with all DNA chemical modifications.
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| Overall design |
Identification of binding sites for 53 transcription factors (52 Arabidopsis thaliana, 1 Zea mays) by direct sequencing of affinity purified genomic DNA fragments. Comparison to ChIP-Seq for ABI5 (AT2G36270).
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| Contributor(s) |
O'Malley RC, Huang SC, Song L, Bartlett A, Galli M, Gallavotti A, Nery JR, Ecker JR |
| Citation(s) |
27203113 |
| |
| Submission date |
Aug 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (1) |
| GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE60143 |
In vitro, genomic context identification of transcription factor binding sites |
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| Relations |
| BioProject |
PRJNA257558 |
| SRA |
SRP045297 |
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