Illumina MiSeq paired end sequencing; Genomic profiling of the FaDu cell line and derived subclones using amplicon-based targeted sequencing
Genomic profiling of the FaDu cell line and derived subclones using amplicon-based targeted sequencing
Cells were seeded in petri dishes and grown until reaching a confluency of 70-80%. Cells were then harvested by trypsination. Genomic DNA (gDNA) was extracted with the Invisorb Spin Tissue Mini Kit (Stratec, Birkenfeld, Germany). HaloPlex library preparation was performed using approximately 225ng of DNA as recommended by the manufacturer (Agilent, protocol version F1, July 2015). Briefly, the gDNA was digested and the HaloPlex probe library was hybridized in the presence of the indexing primer cassette. The biotinylated DNA-probe hybrids were captured by magnetic purification of the samples with streptavidin-coated magnetic beads. Fragmented targets were amplified via PCR at cycling conditions recommended by the manufacturer. Subsequent to the PCR reaction, the final library was purified using AMPure XP magnetic beads (Beckman Coulter, Krefeld, Germany) and quantified using the library quantification kit Illumina TruSeq (Bio-Rad Laboratories, Munich, Germany) and the QX200 ddPCR System (Bio-Rad Laboratories).