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. 2023 Dec 13;624(7991):317–332. doi: 10.1038/s41586-023-06812-z

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a, Left, the transcriptomic taxonomy tree of 338 subclasses organized in a dendrogram (10xv2: n = 1,699,939 cells; 10xv3: n = 2,341,350 cells; 10x Multiome: n = 1,687 nuclei). The neighbourhood and class levels are marked on the taxonomy tree. Classes marked with asterisks are included in the NN–IMN-GC neighbourhood. The IDs of every third subclass are shown to the right of the dendrogram. Full subclass names are provided in Supplementary Table 7. Following subclass IDs, bar plots represent (left to right): major neurotransmitter type, region distribution of profiled cells, number of clusters per subclass, number of RNA-seq cells analysed per subclass, and number of cells analysed by MERFISH per subclass. Subclasses marked with grey dots contain sex-dominant clusters. Sex-dominant clusters within a subclass are identified by calculating the odds and log P value for male/female distribution per cluster. Clusters with odds < 0.2 and log₁₀(P value) < −10 are considered to be sex-dominant. b–e, UMAP representation of all cell types coloured by class (b), subclass (c), brain region (d) and major neurotransmitter type (e). Colour schemes for a–e are shown in the key at the bottom right of the figure. Astro, astrocyte; CB, cerebellum; CGE, caudal ganglionic eminence; CNU, cerebral nuclei; CR, Cajal–Retzius; CT, corticothalamic; CTX, cerebral cortex; CTXsp, cortical subplate; DG, dentate gyrus; EA, extended amygdala; Epen, ependymal; EPI, epithalamus; ET, extratelencephalic; GC, granule cell; HB, hindbrain; HPF, hippocampal formation; HY, hypothalamus; HYa, anterior hypothalamic; IMN, immature neurons; IT, intratelencephalic; L6b, layer 6b; LGE, lateral ganglionic eminence; LH, lateral habenula; LSX, lateral septal complex; MB, midbrain; MGE, medial ganglionic eminence; MH, medial habenula; MM, medial mammillary nucleus; MY, medulla; NN, non-neuronal; NP, near-projecting; OB, olfactory bulb; OEC, olfactory ensheathing cells; OLF, olfactory areas; Oligo, oligodendrocytes; OPC, oligodendrocyte precursor cells; P, pons; PAL, pallidum; STR, striatum; TH, thalamus. Neurotransmitter types: Chol, cholinergic; Dopa, dopaminergic; GABA, GABAergic; Glut, glutamatergic; Glyc, glycinergic; Hist, histaminergic; Nora, noradrenergic; Sero, serotonergic; NA, not applicable (no neurotransmitter detected).