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| Status |
Public on Sep 15, 2008 |
| Title |
Genome-Wide Gli3 Binding Sites in the E11.5 Mouse Limb Bud |
| Organism(s) |
Mus musculus |
| Summary |
Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We have characterized the Gli-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of the developing mouse limb. These analyses identified approximately 5,000 high quality Gli3 binding sites, including all known Gli-dependent enhancers. Discrete binding regions exhibit a higher-order clustering, highlighting the complexity of cis-regulatory interactions. Further, Gli3 binds inertly to previously identified neural-specific Gli enhancers, demonstrating the accessibility of their cis-regulatory elements. Intersection of DNA binding data with gene expression profiles predicted 205 putative limb target genes.
The supplementary bed file contains all 5,274 high quality binding Gli3 binding sites reported in the paper.
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| Overall design |
RosaGli3T-FLAG limb buds ChIPed with FLAG (Gli3-repressor binding sites) vs. Input in E11.5 mouse limb buds.
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| Contributor(s) |
Ji H, Vokes SA |
| Citation(s) |
18832070
|
| Submission date |
Apr 04, 2008 |
| Contact name |
Steven A. Vokes |
| Organization name |
Harvard University
|
| Department |
Molecular & Cellular Biology
|
| Lab |
Andy McMahon
|
| Street address |
16 Divinity Ave
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platforms (8)
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| GPL5811 |
Affymetrix Mouse Promoter 1.0R Array |
| GPL6444 |
Affymetrix GeneChip Mouse Tiling 2.0R Array Set, Array 1 |
| GPL6445 |
Affymetrix GeneChip Mouse Tiling 2.0R Array Set, Array 2 |
| GPL6446 |
Affymetrix GeneChip Mouse Tiling 2.0R Array Set, Array 3 |
| GPL6447 |
Affymetrix GeneChip Mouse Tiling 2.0R Array Set, Array 4 |
| GPL6448 |
Affymetrix GeneChip Mouse Tiling 2.0R Array Set, Array 5 |
| GPL6449 |
Affymetrix GeneChip Mouse Tiling 2.0R Array Set, Array 6 |
| GPL6450 |
Affymetrix GeneChip Mouse Tiling 2.0R Array Set, Array 7 |
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| Samples (15)
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| This SubSeries is part of SuperSeries: |
| GSE11077 |
A Genome-Scale Analysis of the Cis-Regulatory Circuitry Underlying Hedgehog Mediated Patterning of the Mammalian Limb |
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