Whole exome sequencing of colorectal cancer patient derived organoids
Genomic DNA sample were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA). Enrichment probes were designed against the region of interest and synthesized through Twist Biosciences (South San Francisco, CA, USA). Library preparation was performed according to the manufacturer's guidelines.  Briefly, fragmented DNAs were cleaned up and end repaired, as well as adenylated at the 3'ends. Adapters were ligated to the DNA fragments, and adapter-ligated DNA fragments were enriched with limited cycle PCR.  Adapter-ligated DNA fragments were validated using Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer. Adapter-ligated DNA fragments were hybridized with biotinylated baits. The hybrid DNAs were captured by streptavidin-coated binding beads. After extensive wash, the captured DNAs were amplified and indexed with Illumina indexing primers. Post-captured DNA libraries were validated using Agilent TapeStation (Agilent, Santa Clara, CA, USA) and quantified using Qubit 2.0 Fluorometer and Real-Time PCR (KAPA Biosystems, Wilmington, MA, USA).