WGS of canine UC: male bladder tumor
Genomic DNA was quantified using the Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA). NEBNext Ultra DNA Library Prep Kit for Illumina, clustering, and sequencing reagents were used throughout the process following the manufacturers recommendations. Briefly, the genomic DNA was fragmented by acoustic shearing with a Covaris S220 instrument. Fragmented DNA was cleaned up and end-repaired. Adapters were ligated after adenylation of the 3ends followed by enrichment by limited cycle PCR. DNA libraries were validated using a High Sensitivity D1000 ScreenTape on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA) and were quantified using Qubit 2.0 Fluorometer. The DNA libraries were also quantified by real time PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturers instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the NovaSeq Control Software (NCS). Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.