Gene expression profile of healthy control organoids, a Parkinson disease patient specific midbrain organoid carrying a triplication in the SNCA gene and two healthy control organoids co-cultured with either healthy or PD hindbrain organoids

Single nuclei RNAseq was used to characterize the cell diversity in healthy control hindbrain organoids, as well as in PD midbrain organoids. Sequencing of healthy midbrain organoids after co-culture with either healthy or PD hinbrain organoids was used to compare the influence of the healthy versus the disease hindbrain context to the healthy midbrain model. Overall design: Individual organoids were cultured for 2-months. Assembloids were established at age of 1-month and co-cultured for 1 additional month, reaching 2-months of age. After which midbrain orgaonids were separated again. All samples were snap-frozen. Nuclei were extracted, FACS sorted and processed for sequencing.