Multimodal datasets of in vitro dopaminergic neuron differentiation

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.