(A) Dissection scheme of a 9.5 dpc embryo (13-somite stage). An embryo was dissected into four segments [(Fb) forebrain; (Hb) hindbrain; (Tb) trunk; and tail bud] by cutting at the isthmus, first somite, and the last somite. Then, the trunk was further divided into two parts, the somite (Sm) and the spinal cord (Sc). Using Trizol solution (BRL, Bethesda, MD) total RNAs were extracted from each of these body parts and used in cDNA synthesis for profiling template preparation. As a reference, RNA from a whole embryo (Wh) was included in the cDNA pool. (B) The iAFLP profiles and size assignment for each peak showing anatomical distribution of three mouse genes. Expected peak positions of the shortest products (Fb) are indicated with gene names separated by . Sizes for 5-Fam-labeled fragments, assigned by Rox-labeled size markers, are always ∼0.5 nucleotides shorter than true length.