Targeted Bisulfite Sequencing Sample Clauses

Targeted Bisulfite Sequencing. ‌ Genomic DNA of peripheral blood mononuclear cells was collected and purified from breast cancer patients by Xxxxxxx Cancer Institute. The genomic DNA was then bisulfite treated with EpiTect Bisulfite Kit (Qiagen #59104) and amplified for 30 cycles using JumpStart Taq (Sigma P2893) and primers complementary to 3 selected regions of interest covering XXX0, XXXX0, and VPM1 (Supplementary Table 1). The amplified product was fragmented with NEB dsDNA Fragmentase (#M0348A) and purified with 1.5x SPRI beads (Kapa #KK8002) following manufacturer’s directions. The product was then end-repaired and A-tailed and custom TruSeq compatible sequencing adapters synthesized by IDT (Supplementary Table 2, Xxxxxxx et al., 2016) were ligated using the Kapa Hyper Prep Kit (#KK8501). Libraries were amplified for 8 cycles using custom primers and Hifi HotStart ReadyMix polymerase (Kapa #KK8501) (See Figure 5). Adaptor-ligated libraries were quality controlled on an Agilent Bioanalyzer and sequenced on an Illumina HiSeq 4000 using 150bp paired-end sequencing at NYU Genome Technology Center.
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