title: GSM8415618: COLO320DM END-seq; Homo sapiens; OTHER
library_construction_protocol: For WGS, entirely digestion (2 hour) with proteinase K (0.5 mg/ml) and RNase A (0.2 mg/ml) in PBS at 65 ℃, genomic DNA was extracted from cells with phenol:chloroform:isoamyl alcohol (25:24:1, PH 7.8) and precipitated with ethanol. The genomic DNA was resuspended in TE buffer and sonicated (Covaris M220) in AFA milliTUBEs (Covaris. 520045) to obtain 200~500 bp fragments. Sonication parameters: PIP 50, duty factor 10%, cycles 200, processing time 170 s. Then, the DNA was purified using the DNA Clean & Concentrator™-5 (ZYMO, D4004) kit. For END-seq, plugs making, DSB end blunting, A-tailing, ligation of END-Seq adapter 1, DNA shearing and extractio and streptavidin capture of labeled DSB ends, blunting, and A-Tailing ligation of END-Seq adapter 2 were implemented in sequence. The WGS libraries were prepared with the fragmented DNA (1 µg) using the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607). The WGS libraries were sequenced for at least 50 G data with PE150 on NovaSeq 6000. The END-seq library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end (2×150 bp) sequencing on an Illumina Novaseq or HiSeq X Ten platform by Annoroad Gene Technology Co. Ltd.