Multimodal datasets of in vitro dopaminergic neuron differentiation

Widespread application of human pluripotent stem cell (PSC)-derived dopaminergic (DA) neurons for cell therapy or in vitro studies of Parkinson’s disease (PD) requires standardization of cell products. This is currently challenging as there is no gold standard for defining the cell types produced using common differentiation protocols. Here we have generated a large single-cell RNA-sequencing time course (274,483 cells) dataset using two of the most widely used DA differentiation protocols. We supplemented this data with single-cell assay for transposase-accessible chromatin sequencing (244,697 cells). Side-by-side comparison of both multimodal datasets and metanalysis of previously reported single-cell RNA-sequencing datasets from other protocols, altogether amounting to 1,835,801 cells in total, revealed remarkable inter-protocol differences in cell specification trajectories, progenitor and DA neuron cell identities, surface markers for purification, contaminating cell types, and gene regulatory networks. In addition, the single-cell epigenetic profiling pinpointed putative target genes of noncoding genome-wide association studies (GWAS) loci relevant to PD. Our findings have implications for optimizing and standardizing cell products for in vitro studies for PD using human PSCs as well as clinical trials