Organoids were incubated with the appropriate volume of RNA lysis buffer (RNAeasy Plus Mini Kit, QIAGEN) and RNA was isolated following the manufacturer's instructions. Libraries were prepared using the “Illumina stranded mRNA ligation" (ISML) prep, according to Illumina protocol 1000000124518 v01. Libraries were then sequenced on the NovaSeq 6000 (Illumina) yielding approximately 25-35 million, 60-bp, paired end reads for all samples.