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Series GSE11077 Query DataSets for GSE11077
Status Public on Sep 15, 2008
Title A Genome-Scale Analysis of the Cis-Regulatory Circuitry Underlying Hedgehog Mediated Patterning of the Mammalian Limb
Organism Mus musculus
Experiment type Expression profiling by 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. A subset of putative cis-regulatory regions were analyzed in transgenic embryos, establishing Blimp1 as a direct Gli target and identifying Gli-activator signaling in a direct, long-range regulation of the BMP antagonist Gremlin. In contrast, a long range silencer cassette downstream of Hand2 likely mediates Gli3 repression in the anterior limb. These studies provide the first comprehensive characterization of the transcriptional output of a Shh-patterning process in the mammalian embryo and a framework for elaborating regulatory networks in the developing limb.

This SuperSeries is composed of the SubSeries listed below.
Overall design Refer to individual Series
Citation(s) 18832070
Submission date Apr 07, 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 (9)
GPL5811 [Mm_PromPR] Affymetrix Mouse Promoter 1.0R Array
GPL6096 [MoEx-1_0-st] Affymetrix Mouse Exon 1.0 ST Array [transcript (gene) version]
GPL6444 [Mm35b_P01R] Affymetrix Mouse Tiling 2.0R Set, Array 1
Samples (43)
GSM279649 Gli3Genome_mm8_1
GSM279650 Gli3Genome_mm8_2
GSM279651 Gli3Genome_mm8_3
This SuperSeries is composed of the following SubSeries:
GSE11062 Genome-Wide Gli3 Binding Sites in the E11.5 Mouse Limb Bud
GSE11063 Expression data from E11.5 mouse embryonic forelimbs - various mutant conditions or dissected limb domains
BioProject PRJNA107069

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
GSE11077_RAW.tar 6.5 Gb (http)(custom) TAR (of BAR, CEL)
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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