Pioneer-seq of p53
Illumina sequencing libraries were prepared using a two-step PCR method. In the first step, DNA was amplified using four sets of primers designed to offset reads and dephase the libraries during sequencing. The number of PCR cycles used in this step was determined by the DNA concentration of each sample, as measured by qPCR. In the second step, each sample was indexed using Nextera dual indices (Nextera XT index primer 1 (N7xx) and Nextera XT index primer 2 (S5xx)). After each PCR step, the reaction mixtures were cleaned up with AMPure XP beads. The concentration of each sample was then determined using the Invitrogen Quant-iT dsDNA assay kit, and equal amounts of DNA from each sample were pooled for paired-end sequencing on an Illumina NextSeq 2x150. Sequencing and quality control were performed at the University at Buffalo Genomics and Bioinformatics Core.