Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

GLI3 Controls the Proliferative Expansion of Digit Progenitors and Exit toward Chondrogenesis to Constrain the Autopod to Pentadactyly

ABSTRACT: The transcriptome of the anterior handplates of mouse limb buds of Gli3 constitutive and Hoxa13-Cre Gli3 conditional mutant embryos was compared to the transcriptome of limb buds of wild type and Gli3 heterozygote embryos at embryonic day E11.75. All samples carried one copy of the Hoxa13-Cre allele.

ORGANISM(S): Mus musculus

SUBMITTER: Aimee Zuniga

PROVIDER: E-MEXP-3495 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

GLI3 constrains digit number by controlling both progenitor proliferation and BMP-dependent exit to chondrogenesis.

Lopez-Rios Javier J Speziale Dario D Robay Dimitri D Scotti Martina M Osterwalder Marco M Nusspaumer Gretel G Galli Antonella A Holländer Georg A GA Kmita Marie M Zeller Rolf R

Developmental cell 20120329 4

Inactivation of Gli3, a key component of Hedgehog signaling in vertebrates, results in formation of additional digits (polydactyly) during limb bud development. The analysis of mouse embryos constitutively lacking Gli3 has revealed the essential GLI3 functions in specifying the anteroposterior (AP) limb axis and digit identities. We conditionally inactivated Gli3 during mouse hand plate development, which uncoupled the resulting preaxial polydactyly from known GLI3 functions in establishing AP a ...[more]

PMID: 22465667

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Project description:Limb buds were dissected from E10.75 mouse embryos, fixed in 1% formaldehyde for 15 min at room temperature, washed 3 times with cold PBS and stored at -800C. Pools of 16 limb buds were used for each ChIP-chip experiment. ChIP was performed according to (Lee et al., 2006) using 2 ?g of anti-CTCF antibodies (A300-543A, Bethyl Laboratories) and EZview Red Protein G/A Affinity Gel (Sigma). Immunoprecipitated and whole cell extract DNA (input) were treated with RNaseA, proteinase K and purified by 2 rounds of extraction with phenol:chloroform: isoamyl alcohol. ChIP and input DNA were amplified using Ligation-Mediated PCR (Lee et al., 2006). PCR was limited to 15 cycles. 1.5 ?g of ChIP and input DNA were fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix) and hybridized to the Chromosome 2 and X tiling arrays (Affymetrix). Tiling arrays data were quantile normalized within cDNA/genomic DNA or ChIP/ input replicate groups using R packages, STARR and Ringo (Zacher et al., 2010; Toedling et al., 2007). The ratio of probe intensity between the experiment and the control groups were computed considering the median values over replicates. The ratios were smoothened by computing the running medians with a half window size set to 150 bp and a minimum of 5 probes per window. To identify enriched regions a minimum of 3 consecutive probes with a smoothed ratio exceeding a threshold have been considered. The threshold has been fixed by taking the 99th percentile of the estimated null distribution of the ratios. Only ChIP enriched regions with score log2?1.5 and width ?150 bp were considered for further analysis. As a complement, array data were quantile normalized within ChIP/input replicate groups and scaled to medial feature intensity of 500 using TAS software (Affymetrix). For each genomic position, a dataset was generated consisting of all probes mapping within a sliding window of 250 bp. The averaged ratios were plotted along the genomic DNA sequence using Integrated Genome Browser (IGB) software (Affymetrix).

Dataset Information

GLI3 Controls the Proliferative Expansion of Digit Progenitors and Exit toward Chondrogenesis to Constrain the Autopod to Pentadactyly

Publications

GLI3 constrains digit number by controlling both progenitor proliferation and BMP-dependent exit to chondrogenesis.

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