Bisulfite Conversion and Amplification of Genomic DNA

0.5–1 µg of genomic DNA was bisulfite-converted with the Methylamp DNA Modification kit (EPIGENTEK, NY, USA). After the conversion, DNA was amplified using FastStart Taq DNA Polymerase, dNTPack (04738314001, MERCK, Darmstadt, Germany) with the following program: 95°C for 5 min; 4 cycles of 95°C for 1 min, 53°C for 3 min, 72°C for 3 min; 2 cycles of 95°C for 30 s, 55°C for 45 s, 72°C for 45 s; 40 cycles of 95°C for 30 s, 72°C for 1.5 min; 72°C for 10 min. PCR products were purified by QIAquick PCR purification kit (28104, QIAGEN, MD, USA). Further amplicon processing, sequencing, and analysis were performed as described (Sagie et al., 2017b (link)). Primers for amplification of bisulfide converted DNA are described in Supplementary file 1. In the case in which a primer set amplified several subtelomeres, we used sequence differences between the amplified subtelomeres to identify the origin of the PCR product (Supplementary file 1, footnote).