The NIH FACEBASE consortium was established in part to create a central resource 
for craniofacial researchers. One purpose is to provide a molecular anatomy of 
craniofacial development. To this end we have used a combination of laser 
capture microdissection and RNA-Seq to define the gene expression programs 
driving development of the murine palate. We focused on the E14.5 palate, soon 
after medial fusion of the two palatal shelves. The palate was divided into 
multiple compartments, including both medial and lateral, as well as oral and 
nasal, for both the anterior and posterior domains. A total of 25 RNA-Seq 
datasets were generated. The results provide a comprehensive view of the region 
specific expression of all transcription factors, growth factors and receptors. 
Paracrine interactions can be inferred from flanking compartment growth 
factor/receptor expression patterns. The results are validated primarily through 
very high concordance with extensive previously published gene expression data 
for the developing palate. In addition selected immunostain validations were 
carried out. In conclusion, this report provides an RNA-Seq based atlas of gene 
expression patterns driving palate development at microanatomic resolution. This 
FACEBASE resource is designed to promote discovery by the craniofacial research 
community.