Extended Data Fig. 1: Characterization and regional transcriptomic analysis of PVALB and SST interneuron subtypes.

a, Dot plot showing expression of marker genes for each PVALB and SST interneuron subtype. b, Correspondence between subtypes identified in this study and previously defined supertypes⁶. c, Regional transcriptomic differences of PVALB and SST interneurons between MOs and VISp, determined using Emergene (see Methods). Emergene calculates a P value for region-specific gene signatures in individual nuclei via permutation tests. d, Heatmap showing the percentage of cells per subtype with significant regional differences. Subtypes with ≥50% significant cells are annotated with the median P value (calculated by Emergene). n.s., not significant; P ≥ 0.05 *P < 0.05; N/A, not analyzed (cluster size <10). Exact P values are provided in Supplementary Table 3. e, Proportions of all PVALB and SST subtypes in MOs and VISp, complete version of Fig. 1b. f, Intersectional genetic strategy preferentially targeting PVALB–Rorb interneurons, showing their axons concentrated in L4 (n = 4 mice). g, Intersectional genetic strategy preferentially targeting PVALB–Fzd6 interneurons, showing that these interneurons reside in L5b and extend their axons laterally within L5b. Sparse labeling achieved by low-dose tamoxifen administration allowed reconstruction of individual PVALB–Fzd6 morphologies, with one example shown (right), representative of n = 8 mice tested with various Tamoxifen dosages. For f-g, note that both strategies have off-target labeling of L5 PT neurons specifically in SSp regions. Scale bars, 100 µm.