Total RNA from spheroids, organoids, and cell lines was isolated using phenol/chloroform extraction. Libraries were prepared using 50ng total RNA with the NEXTFLEX® Small RNA-Seq Kit v3 (PerkinElmer). The NEXTflex 3' and NEXTflex 5' 4N Adapter were diluted 1:2, and the amplification was performed with 18 cycles. The amplified libraries were purified with AMPure XP beads (Beckman Coulter, Krefeld, Germany) by using a 2:1 bead:sample ratio.