Fig. 1.

Identification of neurogenic niche genes in the adult mouse SGZ. (A) Thionin-stained cryosection of mouse DG showing the subgranular zone (SGZ), located at the base of the granule cell layer (GCL) and adjacent to but separate from the hilus. (B) Schematic representation of the many different known cell types in the SGZ. Also shown are excitatory mossy cells in the hilus and mature granule cells. Corresponding labels share the same color as the cell type. The schematic was derived from labeled cells shown in previously published studies (Amaral, 1978; Claiborne et al., 1986; Jessberger et al., 2008; Kosaka and Hama, 1986; Lawrence and McBain, 2003; Palmer et al., 2000; Seki and Arai, 1999). (C-E) SGZ enrichment for Dcx and Sox11 corroborated by ISH (C,D) and microarrays (E). Dcx and Sox11 ISH also show enrichment in the wall of the lateral ventricle (LV) and rostral migratory stream (RMS). Insets in C,D show high magnification views of the boxed areas. In E, box and whiskers represent 25/75% and 5/95% quantiles, respectively. (F) Highly significant agreement was seen between SGZ-enriched genes found using ISH and microarrays (P<10^-35). y-axis is the density distribution (scaled average count) across paired t-test statistics for regional differential expression between SGZ and GCL (x-axis). Genes confirmed by ISH (red) show a significant skew towards SGZ enrichment relative to those not found in the SGZ using ISH (black). Vertical red and black lines show the mean of each distribution. Scale bars: 100 μm (A); 500 μm (C,D).