Genome wide analysis of chick limb bud tissue treated with FGF2 for 3hrs (RNA-Seq)

During limb development, in addition to proximal to distal outgrowth, FGF regulates a number of factors necessary for SHH expression. To elucidate the molecules involved in FGF-mediated SHH expression we implanted FGF2 beads in HH23 chicken forelimb buds and excised the SHH-expressing tissue for transcriptome analysis. The hypothesis is that this transcriptome data along with data from SHH-expressing tissue after a 24hr treatment would highlight molecules necessary for SHH FGF-mediated SHH expression. Results from the overlap provide a short-list of SHH-related genes which require further testing to assess their role in mediating SHH expression. Total RNA extracted from SHH-expressing chick limb bud tissue following 3hrs of FGF2 treatment compared to PBS-treated controls. Tissue from 15-20 limbs were pooled based on the treatments groups (PBS vs FGF) for each sample. 3 FGF and 3 PBS samples were submitted for RNA-seq analysis.