Figure 2-3
(A, B) Total number of nuclei profiled for each Ex and In subclusters, respectively. (C, D) Percentage of nuclei from each subject for each Ex and In subclusters, respectively. (E) In-situ hybridization images (Allen Brain Institute) showing expression patterns across layers for cortical layer marker genes in the DLPFC and sgACC (http://human.brain-map.org/ish/). Markers FOXP2, TLE4, and CTGF are not shown as they are not available on the Allen Brain Atlas. (F) Scaled mean expression values of inhibitory neuron marker genes for MGE-derived In subclusters. (G) Percent nuclei expression of ganglionic eminence marker genes by each In subcluster. Two distinct expression patterns emerge for In subclusters derived from medial ganglionic eminence (MGE) and for In subclusters derived from caudal ganglionic eminence (CGE). (H) tSNE plots identifying corresponding HBCC Ex subclusters (top plot) to Allen Brain Atlas Ex subclusters (bottom plot). (I) tSNE plots identifying corresponding HBCC In subclusters (top plot) to Allen Brain Atlas In subclusters (bottom plot). (J) RNAscope validation of LHX6+/SST+ cell types in human sgACC and DLPFC sections. LHX6 and SST transcripts were detected with chromogenic RNAscope probes, red and green, respectively. In both the sgACC and the DLPFC LHX6+/SST+ neurons were found throughout the cortex. (K) RNAscope validation of LHX6+/PVALB+ cell types in human sgACC and DLPFC sections. LHX6 and PVALB transcripts were detected with chromogenic RNAscope probes, red and green, respectively. In both the DLPFC and sgACC, LHX6+/PVALB+ neurons were found in cortical layers IV and above. (L) RNAscope validation of HTR2C+/VIP+ neurons in human sgACC and DLPFC sections. HTR2C and VIP transcripts were detected with chromogenic RNAscope probes, red and green, respectively. In both the sgACC and the DLPFC HTR2C+/VIP+ neurons were found throughout the cortex. (M) RNAscope validation of POSTN+/SMYD1+ neurons in human sgACC and DLPFC sections. SMYD1 and POSTN transcripts were detected with chromogenic RNAscope probes, red and green, respectively. POSTN is a gene found to be downregulated in SCZ (Gandal MJ et al., 2018b). In both the sgACC and the DLPFC POSTN+/SMYD1+ neurons were found in the lower-layer. Download Figure 2-3, TIF file.