scRNA-seq analysis of 5 iPSC-derived neuronal subtypes with differential vulnerability to tau seeding

The following single cell dataset includes 5 hiPSC-derived neuronal subtypes derived from a single hiPSC donor line (iPSC0028 MAPT-WT 1B2). The 5 neuronal populations are referred to as cortical inhibitory, cortical excitatory, hypothalamic, midbrain dopaminergic, and hindbrain, based on their marker gene expression determined by a combination of qPCR and IF. In-house tau aggregation assays show the 5 neuronal subtypes display differential vulnerability to tau seeding with AD-brain derived tau seeds. For this study, hiPSC-derived neurons were harvested at DIV14 and two replicates were analyzed per neuronal subtype. Standard QC parameters were employed to remove RNA features detected in < 3 cells, to remove cells where < 200 RNA features are detected, to remove doublets/multiplets, and to estimate and remove contamination in individual cells (decontX). Additionally, cells displaying > 15% mitochondrial transcripts and cells with an intronic ratio > 50% were removed. This dataset will allow users to explore gene expression among the 5 neuronal subtypes in addition to identifying subpopulations within each subtype. It will serve as a valuable reference dataset for current and future studies using these neuronal subtypes.