Fig. 1: Single-cell analysis of chromatin accessibility in the adult whole mouse brain.

a, Schematic of the sample dissection strategy. The brain map was generated using coordinates from the Allen Mouse Brain Common Coordinate Framework (CCF) v.3 (ref. ²⁶). b, The number of nuclei for 117 dissections after quality control and doublet removal. The dot size is proportional to the size of cells and the dissections that were not covered by our previous study¹⁹ are shown in grey. A to L on the left were used as the dissection region labels on each slice (details are provided in Extended Data Fig. 1). The number of dissections represents the number of dissections covered by our previous study (last) and updated in the current study (new). The total number of cells represents the number of cells covered by our previous study (last) and updated in the current study (new). c, UMAP⁸¹ embedding and clustering analysis of snATAC–seq data. The light colours denote major cell classes. NN, non-neuronal cells. Cells are coloured on the basis of major regions as in b. d, The co-embedding UMAP embedding of the neuronal cells from scRNA-seq data⁵ and the snATAC–seq data on the same space coloured by the two modalities. e, The consensus score between neuronal subclasses from the scRNA-seq data above and L4-level neuronal clusters from our snATAC–seq data. f, The 253 neuronal subclasses in our snATAC–seq data matched to neuronal subclasses in the scRNA-seq above, and ordered on the basis of the subclass IDs (for all of the following figures, the order was kept the same unless otherwise mentioned). From left to right, the bar plots represent the class, major neurotransmitter (NT) type, biological replicate distribution of nuclei, major region distribution of nuclei, number of clusters and number of nuclei. Detailed information about class, neurotransmitter type and subclass is reported in the companion paper⁵. A list of full names of the subclasses is provided in Supplementary Table 3. CTX, cerebral cortex; HYa, anterior hypothalamus; L6b, layer 6b; LSX, lateral septal complex; IT, intratelencephalic; ET, extratelencephalic; NP, near-projecting; CT, corticothalamic; OB, olfactory bulb; CR, Cajal-Retzius; DG, dentate gyrus; IMN, immature neurons; CGE, caudal ganglionic eminence; MGE, medial ganglionic eminence; CNU, cerebral nuclei; LGE, lateral ganglioniceminence; MH, medial habenula; LH, lateral habenula; Chol, cholinergic neurons; Dopa, dopaminergic neurons; Glyc, glycinergic neurons; Sero, serotonergic neurons.