Extended Data Fig. 7: Adult piriform cortex immature neurons and the transcriptomic divergence of pyramidal cells between lab and wild mice and between human individuals.
(a) Left: distribution of piriform cortex mature and immature neurons in reanalyzed MERFISH data (Zhang et al.25). Right: cumulative distribution along the anterior–posterior axis of piriform cortex of all pyramidal cells, immature neurons, and pyramidal cells from Yao 2023 aligning with subtype Pyr7 (Yao et al.64; Zhang et al.25). (b) Classification accuracy of support vector machine (SVM) trained on combined RNA and ATAC data of the pPir dataset. Each neuron type is distinguished. (c) Same as (b) but applied to subtypes. Each neuron subtype is distinguished. (d) Conservation scores for aPir, pPir, and SSp. Scores are median probabilities of transcriptomic similarity between lab and wild datasets, quantified by considering all mature neurons, or neurons of a given cell type (SL, Pyr, Vglut2, and IN). A conservation score of 0.5 indicates perfect mixing between lab and wild datasets. 95% confidence intervals (CIs) for each neuron type are reported in brackets. (e) Statistical significance of pairwise differences in conservation score between cortices reported per neuron type (see also (d)). P-values are calculated using two-sided Mann–Whitney U-Tests and Bonferroni-corrected. P-values in red are smaller than α0.01(Bonf.)=8.34e-4, p values in yellow are (only) smaller than α0.05(Bonf.)=4.167e-3. (f) Similarity (as cosine distance) between lab and wild neuron types upon integrating lab and wild pPir datasets using scVI. Pyramidal cells were on average less similar to each other than the other neuron types. (g) Percentage of lab pPir neighbors in scVI integration when computing nearest neighbor graphs from 5 to 100. Data shown as mean +/- bootstrapped 95% CIs, for 7861 aligned (other Pyr cells) and 184 misaligned cells (wild-specific Pyr cells). Alignment of cells between lab and wild datasets is taken from the OT integration shown in (c). (h) Classification accuracy of SVM trained on combined lab and wild pPir data. Neuron types are distinguished with 98.8% accuracy. (i) Immunohistochemistry using lab (left) and wild-derived mice (right) of markers for piriform neuronal populations (in cyan), namely RELN for SL, CUX1 for Pyr, GABA for INs, co-stained with DCX (in magenta), a canonical marker for immature neurons. Inset white boxes with higher magnification show coexpression of CUX1 with DCX in both lab and wild-derived mice. Scale bar, 100 μm. (j) Conservation scores per neuron type for adult human piriform (PIR) and primary somatosensory cortex (S1C) computed using published adult human whole-brain sn-RNA-seq data (Siletti et al.41). Scores are computed per pair of three human donors. Abbreviated donor IDs: h18 for H.18.30.001, h19.1 for h19.30.001, and h19.2 for H19.30.002. Within violin plots, black circles mark medians and black bars indicate 95% CIs. Bonferroni-corrected significance thresholds were α0.01(Bonf.)=1.59e-4 and α0.05(Bonf.)=7.94e-4. IT: intratelencephalic; NP: near projecting (see Supplementary Table 1 for sample size, see (l) for statistical significance). (k) Conservation scores as in (d), but for human piriform (left) and primary somatosensory cortex (right). Scores are median probabilities of transcriptomic similarity per pair of donors. (l) Statistical significance of pairwise differences in conservation score as shown in (e), but between donors. P-values are calculated using two-sided Mann–Whitney U-Tests and reported per neuron type.
