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Series GSE11062 Query DataSets for GSE11062
Status Public on Sep 15, 2008
Title Genome-Wide Gli3 Binding Sites in the E11.5 Mouse Limb Bud
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by genome tiling array
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.
Overall design RosaGli3T-FLAG limb buds ChIPed with FLAG (Gli3-repressor binding sites) vs. Input in E11.5 mouse limb buds.
Contributor(s) Ji H, Vokes SA
Citation(s) 18832070
Submission date Apr 04, 2008
Last update date Jan 29, 2022
Contact name Steven A. Vokes
Organization name University of Texas at Austin
Department Molecular Biosciences
Street address 2500 Speedway, STOP A5000
City Austin
State/province Texas
ZIP/Postal code 78757
Country USA
Platforms (8)
GPL5811 [Mm_PromPR] Affymetrix Mouse Promoter 1.0R Array
GPL6444 [Mm35b_P01R] Affymetrix Mouse Tiling 2.0R Set, Array 1
GPL6445 [Mm35b_P02R] Affymetrix Mouse Tiling 2.0R Set, Array 2
Samples (15)
GSM279649 Gli3Genome_mm8_1
GSM279650 Gli3Genome_mm8_2
GSM279651 Gli3Genome_mm8_3
This SubSeries is part of SuperSeries:
GSE11077 A Genome-Scale Analysis of the Cis-Regulatory Circuitry Underlying Hedgehog Mediated Patterning of the Mammalian Limb
BioProject PRJNA108815

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
GSE11062_GLI3SD6.bed 133.5 Kb (ftp)(http) BED
GSE11062_RAW.tar 6.0 Gb (http)(custom) TAR (of BAR, CEL)
Processed data provided as supplementary file

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