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Here, we provide the Supplementary Material, including detailed Content notes and direct viewing of Supplementary Material Figure 1 and 2, while Supplementary Material Tables 1-3 are available for download. All raw sequencing data generated in this study have been deposited to the CNGB Nucleotide Sequence Archive under accession number CNP0004459. For any questions or inquiries about this work, please refer to the author contact information provided at the end of this page.
Content notes
In the telencephalon, PFC Ex neurons (SLC17A7+) could be further subdivided into layer-specific subtypes including L2/3-IT (intratelencephalic; PDZD2+), L4/5-IT (RORB+), L5/6-IT-Car3 (claustrum-like; RGS12+), L5-IT (TSHZ2+), L5-ET (extratelencephalic; ADRA1A+), L5/6-NP (near-projecting; HTR2C+), L6-CT (corticothalamic; SEMA3E+) and L6-IT (ITGA8+)1,2. Hippocampal non-DG Ex neurons clustered according to their subanatomical location including the CA1/SUB (cornu ammonis subfields 1 and subiculum; PID1+), CA2/4 (cornu ammonis subfields 2 , 3 and 4; NRIP3+), and entorhinal cortex (EC) that was subdivided into upper layer (L2, CUX2+ RXFP1+; L3-5, TLL1+ PCP4+) and deep layer (L6, TLE4+ NXPH2+) neurons1,3,4. Additionally, the CA1/SUB subpopulations could be further subdivided according to the superficial-deep axis (CA1/SUB: superficial CCBE1+ and deep NDST4+). Among the Inh neurons, we identified subpopulations derived from the medial ganglionic eminence (MGE; LHX6+), caudal ganglionic eminence (CGE; ADARB2+), and lateral ganglionic eminence (LGE; FOXP1+)5. MGE-derived Inh neurons were distributed in all telencephalic regions, CGE-derived Inh neurons were mainly in the PFC and hippocampal formation, and LGE-derived Inh neurons in the striatum. MGE-derived Inh neurons could be further subdivided into PVALB+ and SST+ in the PFC and hippocampal formation, as well as SST+, TAC3+ and CRABP1+ in the striatum. We also noticed a small cluster of MGE-derived UNC5B+ chandelier cells in the PFC. CGE-derived Inh neurons contained LAMP5+ and CNR1+. LGE-derived Inh neurons were composed of spiny projection neurons (SPNs;MEIS2+) including subtypes expressing the D1-type (SPN-D1; TAC1+) or D2-type (SPN-D2; PENK+) dopamine receptor, and eccentric SPNs (RBM20+). SPN-D1 contained a cluster belonging to neurochemically unique domains in the accumbens and putamen (SPN-D1-NUDAP; RXFP1+). In addition, we identified granule cells from the islands of Calleja (ICj) in the ventral striatum (ICj Inh; CPNE4+)6.
In the thalamus, we observed TPH1+cells and a cluster of Ex neurons (SLC17A6+) comprising RYR3+ and CBLN2+ subtypes. RYR3+ neurons correspond to cortex-projecting neurons distributed in the ventral lateral and ventral anterior thalamus7, while CBLN2 is highly expressed in motor-related nuclei8. We also noticed GAD2+ SST+ Inh neurons characteristic of the thalamic reticular nucleus9, and GAD2+ OTX2+ midbrain-derived Inh neurons in the thalamus,midbrain and pons and medulla10. Likewise, there were A9 (SOX6+) and A10 (CALB1+) subtype dopaminergic (DA) neurons (TH+) in the midbrain11, and in the pons and medulla Ex neurons including upper rhombic lip and lower rhombic lip neuron10. In the cerebellum, besides cerebellar granule cells (GCs), we observed Purkinje cells (PPP1R17+), molecular layer interneuron (MLI1/2;LYPD6+; CALB1+), Purkinje layer Inh (PLI; KLHL1+) neurons and unipolar brush cells (UBC; EOMES+)12.
Notably, the splatter neuron appeared in the non-telencephalic regions. To explore this population further, we combined those cells together and reclustered, obtaining a total of 18 clusters. These included: SLC24A2+ glutamatergic neurons; SLC32A1+ GABAergic neurons; CALCR+ (calcitonin receptor) neurons; TAC1+ (encodes preprotachykinin-1) neurons; SST+ (encodes somatostatin) neurons; PENK+ (encodes proenkephalin) neurons; CRHBP+ (encodes corticotropin-releasing hormone-binding protein) neurons; CARTPT+ (encodes cocaine- and amphetamine-regulated transcript prepropeptide) neurons; TRH+ (encodes thyrotropin-releasing hormone) neurons; TRHR+ (encodes thyrotropin-releasing hormone receptor); CRH+ (encodes corticotropin-releasing hormone); POMC+ (encodes proopiomelanocortin) population; histaminergic neurons (HDC+) that are located in ventral posterior hypothalamus; TPH2+ (encodes tryptophan hydroxylase 2) neurons; PMCH+ (encodes pro-melanin concentrating hormone) neurons; AVP+ (encodes arginine vasopressin) neurons; HCRT+ (encodes hypocretin neuropeptide precursor) neurons; OXT+ (encodes oxytocin) neurons.
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Supplementary Material Figure 1
(A-E) Left: Schematic representation of major anatomical regions in a hemibrain section (section H7) from a 6-year-old macaque monkey, alongside spatial visualization of astrocytes (Ast1-3), microglia (Mic1-3, macrophages), oligodendrocytes (ODC1/2) and oligodendrocyte progenitor cells (OPC1/2, COPs) subtypes, mapped to the same anatomical section using Stereo-seq data from Chen et al., Cell 2023. Right: Bubble plots showing the expression levels of representative marker genes for each cell subtype. Color scale represents scaled average gene expression, while dot size indicates the percentage of cells expressing a given marker within the corresponding cell subtype.
Supplementary Material Figure 2
Bar plots showing the overlap between DEGs across all cell subtypes for four comparison groups, with unique sDEGs (blue), shared DEGs (green), and unique pDEGs (red).
Accessions
CNP0004459
Contact
miguelesteban@genomics.cn;
laiyiwei@genomics.cn;
zhangxiao6@genomics.cn;
laiguangyao@genomics.cn