We assayed ~25 areas of the developing neocortex, delineating nine layers per area (here referring to fetal mitotic and postmitotic zones and not layers 1–6 of mature neocortex)29: SG, marginal zone (MZ), outer and inner CP (CPo; CPi), SP, IZ (or inner SP), outer and inner SZ (SZo; SZi), and VZ (Fig. 2a). Approximately 95% of RefSeq genes are expressed in developing neocortex, compared with 84% identified using these arrays in adult23. Different layers show robust and unique molecular signatures, and samples group by layer using hierarchical clustering (using differential genes from ANOVA, p<10−29) at both timepoints (Fig. 2b). Samples also cluster with multidimensional scaling (MDS), where dimension one separates samples by layer, with germinal zones (VZ, SZi, SZo) distinct from layers containing primarily postmitotic cells, and dimension two roughly reflects rostrocaudal position (Fig. 2c).
