Fig. 1. A genomics-based investigation into the nature and composition of a neocortical protomap successfully identified genes with described spatial differences in expression. (A) Strategy for a genomics-based identification of protomap components. Rostral and caudal thirds of the neocortex were dissected from mouse embryos at two ages (E11.5 and E13.5) in both inbred and outbred strains. Comparison of gene expression between rostral and caudal tissue was carried out within single litters of embryos to reduce variability in the developmental stages of embryos. In addition to spatial gene expression, the same samples were also used to analyse temporal changes in gene expression. (B) Screen efficacy was demonstrated by the successful identification of almost all of the genes that have been previously described as having differential rostrocaudal expression, including COUP-TFI, Lhx2, Sfrp1 and Pax6. Plots of gene expression ratios (expressed in base 2) between rostral and caudal neocortex are shown. The graphs show changes in gene expression for single genes for multiple dye-swapped samples. The stage and strain of origin of the samples is as indicated, with each datapoint representing a measurement from a single microarray. Measurements are presented as dye-swapped pairs, producing the alternating positive and negative expression patterns. The two caudally expressed genes COUP-TFI and Lhx2 show an opposite expression pattern to the two rostral genes Sfrp1 and Pax6.