Figure 3. Cell type enrichment of TFs and co-factors.

(A) Heatmap of expression of TFs, co-factors, and chromatin remodelers enriched in RG, excitatory neurons, and deep layer excitatory neurons. Cells are grouped by cluster. Red indicates factors previously unknown to be enriched in the neocortical cell types of interest. (B) Expression of factors of interest in bulk tissue LCM laminae from developing cortex. (C) RNA FISH of fetal cortex probed with the newly identified cell-enriched TF ZFHX4 (neural progenitors in the VZ and SVZ), and known markers PAX6 (RG marker) and EOMES (IP marker). Insets show higher magnification of the VZ and SVZ. (E) Quantification of the percentage of PAX6+ or EOMES+ cells co-expressing ZFHX4. ZFHX4 is expressed in both RG and IPs. (F and G) RNA FISH of fetal cortex probed with the newly identified cell-enriched TFs CARHSP1 (neural progenitors in the VZ and SVZ), and CSRP2 (glutamatergic neurons in the CP). (C, D, F, G) Quantification of normalized fluorescence intensity per layer for each set of probes (see materials and methods). Scale bar = 250μm (left) or 100μm (inset). (H) Schematic of cell-type specific expression of factors of interest. Color indicates -log₁₀ p-value from Fisher’s test.