To prepare scRNA-seq libraries from NGN2-iN single-cell suspensions, Chromium Single-cell 3′ Reagent Kits (10× Genomics, Pleasanton, CA, USA) were applied according to the manufacturer’s instructions. The Chromium Single-cell 3′ Reagent Kits v.2 was employed on NGN2-iN generated from 409B2 time course experiments, monoclonal 409B2 and Sc102a1 iPSCs with approximately 3,000 cells loaded per lane on a 10x microfluidic chip device. Chromium Single-cell 3′ Reagent Kit v.3 was used on Dox treatment duration experiments with nearly 8,000 cells loaded per lane. Quantification and quality control of the 10× library was carried out on a Bioanalyzer (Agilent) using high-sensitivity DNA chips. Libraries prepared from the 10× v.2 kit and v.3 kit were respectively sequenced on the Illumina HiSeq 2500 and Illumina NovaSeq S1 platform.
