RNA was collected every 24 hours over the 5-day differentiation period. Total RNA collection included a digestion step using DNase I, extracted using Direct-zol™ RNA MiniPrep kit (Zymo Research). RNA quality and quantity were checked using Agilent RNA Screen Tape on the Agilent Tapestation. For Illumina (short-read) sequencing libraries were prepared from 150 ng RNA, using an Illumina TruSeq Stranded mRNA Library prep kit following the manufacturer's protocol (Illumina, Cat#20020594). For Nanopore (long-read) sequencing, 75 ng of RNA were used to prepare the sequencing library using a cDNA-PCR Sequencing Kit (SQK-PCS109) following the manufacturer's protocol (Oxford Nanopore).