library_construction_protocol: Organoids cultured in soft and stiff  hydrogels were collected. Total mRNA was extracted using TRIzol (Life Technologies) followed by purification by an RNeasy Mini Kit (QIAGEN). RNA-seq libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina), then samples were sequenced by an Illumina HiSeq 2500 sequencer. 