title: Illumina whole genome sequencing of bile sample from gallstone patients
design: Without centrifugation of bile samples, total DNA of 400 μL bile per patient was extracted using Invitrogen Purelink Genomic DNA mini kit (Life Technologies, Carlsbad, CA, USA), following manufacturer’s blood DNA extraction protocol. DNA concentration was quantified by Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), and quality was examined by agarose gel electrophoresis using E-Gel electrophoresis system (L ife Technologies, Carlsbad, CA, USA). Total DNA of bile samples was sheared into ~350bp fragments by Covaris M220 (Covaris, Woburn, MA, USA) and then multiplexed libraries were prepared using Illumina TruSeq Nano DNA Sample Preparation Kits (Illumina, San Diego, CA, USA) according to manufacturer’s instructions. Illumina HiSeq 2000 platform was used to generated 2x100 bp pair-end sequencing reads.