Figure 4. Cell types summary and relationships.

(a–c) Constellation diagrams showing core and intermediate cells for all cell types. Core cells (N = 1424 total, 664 GABAergic, 609 glutamatergic, 151 non-neuronal) are represented by colored discs with area corresponding to the number of core cells for each cluster. Linked tags include cell type names based on marker genes/layers; unique markers are in pink. Intermediate cells (N = 255 total, 97 GABAergic, 155 glutamatergic, 3 non-neuronal) are represented by lines connecting discs; line thickness corresponds to the number of such cells. (a) GABAergic neuron types are grouped according to major classes and arranged by their preferential location (enrichment) in upper vs. lower cortical layers. Up/down arrows within discs represent statistically significant enrichment determined by layer-enriching dissections (Supplementary Table 5). Locations for other clusters are estimates that combine marker gene expression or Cre line expression based on ISH. The position at the border of upper and lower layers represents lack of evidence for location preference. (b) Glutamatergic types are arranged according to cortical layer. (c) Non-neuronal types share few intermediate cells among one another. 96*Rik, 9630013A20Rik. (d) Dendrogram depicting relatedness of the mean gene expression pattern for all cell types based on core cells (N = 1424) and genes (N = 13,878) with standard deviation for expression > 1 across all types. The distance metric is Pearson’s correlation coefficient over the genes in the log₁₀(RPKM+1) space. The tree was generated by standard hierarchical clustering with average linkage.