Bile acid species detection and quantification

Bile acid profiling was performed as described previously (Zhu et al., 2018). For liver tissue samples, livers were homogenized in water (100 mg tissue in 500 μL water), and then 300 μL of methanol: acetonitrile (v/v, 1:1) was added to a 100 μL aliquot of liver homogenate. For serum samples, 25 μL serum was mixed with 100 μL of methanol: acetonitrile (v/v, 1:1). All the mixtures were vortexed for 2 min and centrifuged at 15,000 rpm for 10 minutes. Two microliter of the supernatants from all samples was injected into the ultra-performance liquid chromatography (UPLC) coupled with a SYNAPT G2-S quadrupole time-of-flight mass spectrometry (Waters Corporation, Milford, MA) for analysis. The column type is Acquity UPLC BEH C18 column (2.1 × 100 mm, 1.7 μm). The details of mobile phase gradient were reported previously (Jiang et al., 2015). The QTOFMS system was operated in a negative high-resolution mode with electrospray ionization as described previously (Zhu et al., 2018). Bile acid species were quantified by measuring their relative abundance as the area under the curve for each species using standards for comparison. WT and YAP1 KO liver samples or serum samples were compared using a t test followed by Benjamini-Hochberg correction for multiple hypothesis testing, using FDR < 0.1 as a cutoff for significance.