Transcriptomics

Dataset Information

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Expression data from E11.5 mouse embryonic forelimbs - various mutant conditions or dissected limb domains


ABSTRACT: 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. In this dataset, we include the expression data obtained from dissected mouse forelimbs using a variety of gain- and loss-of-function hedgehog pathway mutants, as well as limbs dissected into responsive (posterior 2/3ds) and non-responsive (anterior 1/3d) Hh tissues. These data are used to obtain 753 genes that are differentially expressed in response to Shh signaling. Keywords: Comparison of genetic samples 28 Total samples were analyzed. We generated the following pairwise comparisons using PowerExpress: ShhWT; Gli3WT; AntPost. Genes with an FDR≤10% and a fold-change ≥2 were selected. We did not generate pairwise comparisons for a certain combinations with SmoGli3 and Gli3 mutants because data from these arrays contained significant variability. To identify additional genes that were Shh-responsive, we performed the following multiple sample comparisons using an FDR≤10% and a posterior probability cutoff of ≤25%: 1.) AntSmoGli3, 3.) AntSmoGli3

ORGANISM(S): Mus musculus  

SUBMITTER: Steven A. Vokes  Steven A Vokes   Hongkai Ji    

PROVIDER: E-GEOD-11063 | ArrayExpress | 2008-09-14

SECONDARY ACCESSION(S): GSE11063PRJNA108817

REPOSITORIES: GEO, ArrayExpress

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Publications

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb.

Vokes Steven A SA   Ji Hongkai H   Wong Wing H WH   McMahon Andrew P AP  

Genes & development 20081001 19


Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We characterized the Gli-dependent cis-regulatory network through a combination of whole-genome chromatin immunoprecipitation (ChIP)-on-chip and transcriptional profiling of the developing mouse limb. These analyses identified approximately 5000 high-quality Gli3-binding sites, including all known Gli-dependent enhancers. Discrete binding regions exhibit a higher-order clusterin  ...[more]

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