Our analysis revealed 190 genes differentially expressed (DE) among PCPs with each gene expressed at >50uTPM (unique transcript per million), >4 folds enrichment and with p-value <5×10−4 (Figure 1D and Table S1). We confirmed known markers for MGE- and CGE- derived interneurons and the 6 PCPs (Figure 1E). We further profiled CHCs from upper (L2/3, CHC1) and deeper (L5/6, CHC2) layers and identified ~11 genes enriched in CHC2 over CHC1 (Figure 1F and Table S1). We validated PCP specific expression of ~10 transcripts by mRNA in-situ hybridization (Figure 1G and Figure S2A). We discovered a putative pan-CHC transcript Pthlh: ~95% of RFP-labeled CHCs were positive for Pthlh (136/143 cells) and their laminar distribution recapitulate CHC pattern in frontal cortex (Figure 1G, Figure S2A). To validate CCK expression in CHCs (Figure 1E), we demonstrate that an intersection of Nkx2.1-Flp and CCK-Cre labeled CHCs at L1, L2 border (Figure 1H).
