Fig. 1. Single nuclei RNA-sequencing of postmortem brain to identify specific cell types in human striatum.

a Post-mortem human brain cohort design and analysis to compare unaffected comparison (UC) individuals with individuals with opioid use disorder (OUD). b Schematic of the sample collection process to isolate single nuclei and generate single nuclei RNA-sequencing libraries in balanced batches from the caudate and putamen of human postmortem striatum. c Per-sample quality control (QC) metrics and average per-nuclei QC metrics across tissue sources and diagnoses. Each data point consists of N = 22 caudate and putamen samples from M = 12 individuals. d Single nuclei clustering and label annotation of dorsal striatal cell types using a high-quality non-human primate reference dataset³⁶. A low dimensionality projection of striatal cell types after QC filtering and annotation. e Dot plots of the marker genes used to annotate the various cell types of the dorsal striatum based on a non-human primate reference. The normalized expression patterns are averaged across all cells and individuals. f Boxplot showing the relative percent of each cell type detected in each biospecimen that passes QC. No significant differences were observed between UC individuals and individuals with OUD. Each data point consists of N = 22 caudate and putamen samples from M = 12 individuals. g Cell type-specific marker genes and (h) marker transcription factor-gene regulatory networks identified in cell types of human striatum. Schematics in (a) and (b) created using BioRender.com. Source data are provided as a Source Data file. Boxplots in 1 C and 1 F are plotted as median, the 25% and 75% percentiles, and non-outlier maxima and minima.