title: HCC70 K14 Negative
design: For whole-genome sequencing HCC70 cells were stained for K18 and K14, and cells were FACS sorted to isolate K18+K14 and K18+K14+ populations. Genomic DNA was extracted using phenol-chloroform following reversal of cross-linking by boiling, and fragmented to a target size of 200bp using a Covaris E220 system. Libraries were prepared using the NEBNext Ultra DNA Library Preparation Kit for Illumina and the Multiplex Oligos Kit for indexes (New England Biolabs), using 100ng of DNA for each sample. The final libraries were quantified by Qubit and library size determined using the Agilent TapeStation 2200. Paired-end sequencing was performed using the NextSeq 500 High Output v2 kit (75 cycles) as described by the manufacturer, with an average Q30>91%. A mean coverage of 2.17x and 2.71x was achieved for the K18+K14 and K18+K14+ DNA, respectively. Alignment was done to the reference genome (hg19) using the BWA-ALN algorithm, with >96% of reads mapped.