Figure 2. Five molecularly distinct interneuron categories defined by scRT-PCR.

a) Six example cells whose genes were amplified by scRT-PCR. Cells are categorized according to their primary (black) and secondary (gray) gene expression: cell1-Pvalb/Tac1, cell2-Sst/Pdyn/Grin3a, cell3-VIP/Tac2, cell4-Tnfaip8l3/Sema3c, cell5-undefined, cell6-Pvalb/Sst/VIP/Tnfaip8l3 (discarded). Full-length gels are presented in Supp. Fig. 2a.

b) Histogram of coexpression of primary and secondary markers from the analysis of 474 single cells (n=474 cells; n=415 slices; n=134 mice). Matching primary and secondary markers are illustrated in the same color.

c) Dichotomous categorization scheme of postsynaptic interneurons based on primary and secondary marker expression. Numbers in brackets represent the percentage of cells categorized according to the scheme (PM = primary marker, SM = secondary marker, UD = undefined).

d) Expression pattern of nine marker genes (four primary and five secondary markers) in 474 cells. Each row is a different cell; each column is a different gene. The color of the primary markers is the same as the color of the co-expressed secondary markers. Cells are sorted and grouped in different categories (labeled on the right) according to their primary and secondary expression pattern.

e) Schematic of genetically defined 3 presynaptic interneuron classes and 6 postsynaptic interneuron categories. The L1 interneuron category contains all unidentified (UD) neurons located in layer 1.