For bulk RNA-seq, total RNA samples were isolated from ESCs or whole organoid samples using the RNeasy Mini Kit. hMGEOs or hCOs were collected from different culture wells and combined for RNA isolation after 30 (12 hMGEOs and 11 hCOs) and 72 (8 hMGEOs and 8 hCOs) days of culture. Libraries were constructed using Tru-Seq RNA library preparation kits, followed by sequencing in HiSeq 2000 with manufacture's protocol.
