On day 6, organoids were released from the ECM, and total RNA was extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions. Whole-transcriptome libraries were generated using the SMART-Seq mRNA kit (Takara Bio) based on the SMART (Switching Mechanism at the 5′ End of RNA Template) method. cDNA libraries were purified using AMPure XP beads (Beckman Coulter). Tagmentation and adapter ligation were performed using the Nextera XT DNA Library Prep Kit (Illumina) together with Illumina DNA-RNA UD Indexes. Pooled libraries were sequenced on an Illumina NovaSeq X Plus system.