RNA-seq analysis of hilar and peripheral biliary organoids from a mouse model of Alagille syndrome

To study molecular differences in wild-type and regenrated bile ducts in a mouse model of Alagille syndrome (Andersson, Chivukula, Hankeova, et al. Gastroenterology, 2018;154(4):1080-1095), we derived intrahepatic cholangiocyte organoids from hilar (pICOs) and peripheral (pICOs) regions of adult livers following a published protocol for organoids derivation and culture (Broutier et al., Nat Protoc. 2016;11:1724–1743). At passage 5, we isolated total RNA and performed bulk RNA-sequencing on 3 biological replicates from each region and genotype. Overall design: Organoids were grown in Matrigel domes. At passage 5, RNA was collected using RNeasy Plus micro kit (Qiagen, 74034), sequencing library was prepared using TruSeq RNA SMP prep Kit-v2 SetA from Illumina (RS-122-2001) and it was sequenced on Illumina NextSeq 550 platform.