Strand-seq data: Sample AG16782
Strand-seq data were generated from lymphoblastoid cell lines. After culture with BrdU for 24h, formaldehyde fixed nuclei with BrdU in the G1 cell cycle phase were enriched by FACS after staining with Hoechst 33258 and Propidium Iodide. Single-nuclei isolation and nanoliter reagent dispensing into the wells of a 5184-nanowell array was performed. Briefly, formaldehyde cross-linking of nuclei was reversed by heat and structural nuclear proteins were digested by a heat-labile protease. Restriction enzymes AluI and HpyCH4V were used for fragmenting genomic DNA and Hemo KlenTaq was used for A-tailing. Fragments were ligated to forked adapters, UV-irradiated, and PCR-amplified with index primers pre-spotted into nanowells before library preparation. Strand-seq libraries were size-selected with AMPure XP beads and 300 to 700 base-pair fragments were gel purified prior to PE75 sequencing on the NextSeq 550. Informative libraries were selected in-silico downstream.