Single cell RNA-seq of Sox9-deficient intrahepatic biliary epithelial cells

To define the regulatory role of Sox9 in intrahepatic biliary epithelium, we conducted single cell RNA-seq on biliary epithelial cells (BECs) from adult control (Sox9fl/fl) and conditional Sox9 knockout (Sox9cKO; Sox9fl/fl:Albumin-Cre) mice. Livers were dissociated to single cells and BECs isolated by FACS based on CD326 positivity. CD31+ and CD45+ cells were excluded by FACS. Gallbladder and extrahepatic tissues were excluded by dissection. Sorted cells were fixed according to manufacturer instructions using Parse Whole Cell Fixation kit. Fixed cells were frozen and stored at -70C for less than 6mo, prior to being used in split-pool combinatorial barcoding according to manufacturer instructions. Barcoding and library construction was carried out with the Parse Evercode Whole Transcriptome v2 kit. Clustering and differential expression analysis of Sox9cKO and control samples of biliary epithelial cells