Extended Data Fig. 8: Transcriptomically-defined cell types across cortical areas of wild-derived mice.

(a) Relative abundance of main cell types across biological replicates (donors) integrated from single-nucleus RNA (sn-RNA-seq) and multiome (sn-multiome seq) sequencing experiments. Replicates IDs 1 and 2 derive from sn-multiome seq experiments, replicates IDs 3, 4, 5 and 6 derive from sn-RNA-seq experiments. From left to right: aPir replicates, indicated by A; pPir replicates, indicated by P; SSp replicates, indicated by N. Numbers correspond to the ID of the donor mouse. W: wild. (b) Post-hoc histological assessment of aPir, pPir, and SSp dissections from anterior and posterior coronal sections of adult wild-derived mice ordered by ID mouse number. Asterisks indicate the microdissected area. Neurotrace counterstain in gray. (c) Left: number of genes per nucleus quantified for biological replicates. A indicates aPir replicates, P indicates pPir, N indicates SSp. Numbers correspond to the ID of mice. Right: number of genes per nucleus identified for main cell types. (d) Same as in (c) but for the fraction of mitochondrial content per nucleus. (e) From left to right: UMAPs of aPir, pPir, and SSp datasets color-coded by main cell types. (f) Gene expression levels of representative markers for each cell type across the three cortical areas, from left to right: aPir, pPir, and SSp. (g) Optimal transport (OT) alignment of main cell types between lab and wild datasets for each cortical area, from left to right: aPir, pPir, and SSp. Color and size of dots indicate the probability of alignment.