Biliary-Columnar-Epithelial-IntraHepatic-HIhBEC-A
Genomic DNA from healthy human cell-types within tissues were extracted with DNeasy Blood and Tissue Kit (Qiagen; Germantown, MD) following the manufacturer's instructions and quantified via Qubit fluorometer dsDNA BR Assay Kit (ThermoFisher Scientific, Cat. No. Q32853). Genomic DNA was fragmented via sonification using a Covaris M220 instrument to the recommended target 150-200 base pairs and then Whole Genome Bisulfite Sequencing libraries were generated using the Zymo Research Pico Methyl-Seq Library Prep Kit (#D5455 Zymo Research, Irvine, CA). WGBS libraries were quantified using KAPA Library Quantification Kits for Illumina Platforms (Kapa Biosystems; Wilmington, MA) and then pooled to meet the required 1ug DNA input necessary for targeted enrichment. Hybridization capture was carried out according to the SeqCap Epi Enrichment System protocol (Roche NimbleGen, Inc.; Pleasanton, CA) using xGen Universal Blocker-TS Mix (Integrated DNA Technologies, USA) as the blocking reagent and SeqCap Epi CpGiant probe pools. MethylC-Capture Sequencing (MCC-seq) libraries were assessed using Qubit Fluorometer (ThermoFisher) and Agilent Bioanalyzer DNA 1000 assays (Agilent Technologies, Inc., USA). MCC-seq libraries with inclusion of 15-20% spike-in PhiX Control v3 library (Illumina; San Diego, CA) were clustered on a Illumina Novaseq 6000 S4 flow cell followed by 150-bp paired-end sequencing.