GSM9075918: DNAseq_ChIPseq_c483_3hr_repB; Homo sapiens; OTHER
genomic DNA was extracted using the AllPrep genomic DNA/RNA extraction kit (Qiagen) Two custom biotin-tagged capture panels (xGen DNA panels, Integrated DNA Technologies) were designed to enrich specific DNA regions, each featuring 120 bp probes with one to four probes flanking each targeted cut site, see Supplemental Table S5-6. One panel contained 402 probes (mtg142) and another contained 979 probes (mtg483). The degeneracy of genomic sequences around cut sites prevented the design of probes with high enough specificity to target all sites, therefore only probe/site combinations which could be targeted without significant overlap were included in the panel. Following library construction, the prepared libraries were hybridized with the panels according to the manufacturer's guidelines, subjected to stringent washes to remove nonspecific fragments, and subsequently PCR-amplified. The enriched libraries were purified and assessed for quality with a tapestation prior to sequencing. Sequencing was multiplexed and performed on a MiSeq 2000 with 10% PhiX spike-in.