Gene expression profiling of the mandibular arch in mice with a conditional inactivation of Alk5 at embryonic day E11.5

We performed global gene expression analyses of the mandibular arch in Alk5^fl/fl ; Wnt1-Cre and Alk5^fl/fl control mice at embryonic day E11.5. Total RNA samples (1 ug per sample) were converted into biotin-labeled cRNA using the GeneChip® IVT Labeling Kit and standard protocols recommended by Affymetrix (Santa Clara, CA). Fragmented cRNA was applied to GeneChip, Mouse Genome 430 2.0 Arrays (Affymetrix) that contain probe sets designed to detect over 39,000 transcripts. Microarrays were hybridized, processed and scanned, as previously described using manufacturers recommended conditions.