Nucleus versus gene UMI count matrix across multiple distinct non-human primate brain regions from single-nucleus RNA sequencing

To comprehensively characterize molecular and cellular organization of brain networks, we establish a large-scale cell atlas of non-human primate brains based on 39 samples from 10 brain regions of two young (6 years old) and two aged (17–24 years old) rhesus macaques using single-nucleus RNA sequencing. The ten brain regions include amygdala (AMY), putamen (PU), hippocampus (HIP), thalamus (TH), dorsolateral prefrontal cortex (DLPFC), cingulate gyrus (CG), superior temporal gyrus (STG), superior parietal lobule (SPL), visual cortex V4 (V4), and cerebellar cortex (CBC). snRNA-seq data were obtained using the DNBelab C4 droplet-based platform following the manufacturer’s protocol. In brief, frozen tissues were unfrozen, minced and isolated into nuclei suspensions. snRNA-seq libraries were prepared using DNBelab C Series Single-Cell Library Prep Set (MGI, 1000021082) and sequenced on the DNBSEQ platform at the China National GeneBank (Shenzhen, China). Raw sequencing reads were first filtered and demultiplexed using PISA (v0.2-17-g8cc39ef). Retained reads were aligned to the Macaca mulatta reference genome (Mmul_10) using STAR (v2.7.9a). Nucleus versus gene UMI count matrix was generated using PISA (v0.7) with GTF annotation file from Ensembl (v102).