library_construction_protocol: Total RNA: AG09429 passage # were trypsinized and pelleted in 1X PBS. Nuclear RNA: the NPCs (GM03440, P7-12) were trypsinized and pelleted, followed by lysis using Nuclei EZ Lysis kit (Sigma). Extracted nuclei were washed in 1X PBS containing 1.0% BSA and 0.2U/μl RNase inhibitor. Total RNA: The cDNA libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per the manufacturer's instruction. Nuclear RNA: library was prepa  red with the Chromium™ Single Cell 3' Library & Gel Bead Kit v3.1 (10x Genomics, PN - 1000121) Total RNA: The libraries were pooled and diluted to 3 nM using 10 mM Tris - HCl, pH 8.5, and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read. Single cell nuclear RNA: NovaSeq 6000 (Illumina) was used to sequence 28 bases for Read 1, 91 bases for Read 2, and 8 bases for Index 1 read, respectively