title: GSM8415762: ssHi-C Scc1-depleted DSB 4 hr; Saccharomyces cerevisiae; OTHER
library_name: GSM8415762
library_construction_protocol: Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm. Hi-C and ssHi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells, with addition of the annealing oligonucleotide mix at 7 nM each in the lysis buffer prior to incubation at 62°C for 10 minutes. DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions. For ssHi-C, two rounds of targeted capture using the IDT xGen Hybridization buffer and enhancer using biotinylated oligonucleotides at 0.6 uM each. The library was digested with MfeI and SspI in NEB cutsmart buffer prior to sequencing.