Fate specification of GFAP-negative primitive neural stem cells and their progeny at clonal resolution

The mature brain contains an incredible number and diversity of cells that are produced and maintained by heterogeneous pools of neural stem cells. Two distinct types of neural stem cells (NSCs) exist in the developing and adult mouse brain: GFAP (Glial Fibrillary Acid Protein)-negative primitive (p)NSCs and downstream GFAP-positive definitive (d)NSCs. To better understand the embryonic functions of NSCs, we performed clonal lineage tracing within neurospheres grown from either pNSCs or dNSCs to enrich for their most immediate downstream neural progenitor cells (NPCs). These clonal progenitor lineage tracing data allowed us to construct a hierarchy of progenitor subtypes downstream of pNSCs and dNSCs that were then validated using single cell transcriptomics. Further, we identify Nexn as required for neuronal specification from neuron/astrocyte progenitor cells downstream of rare pNSCs. Combined, these data provide single cell resolution of NPC lineages downstream of rare pNSCs that likely would be missed from population level analyses in vivo.