GSM7325027: HiC_501mel shLuc 6D rep 1; Homo sapiens; Hi-C
Arima Hi-C kit (Arima genomics) was used for all Hi-C experiments. Standard input protocol was followed with 3 x 106 cells for each condition. Proximally ligated DNA was fragmented to around 400bp by Covaris E220 focused ultrasonicator (peak power = 140 W, duty factor = 10%, cycle per burst = 200) for 70 sec. Fragmented DNA was sized selected to have a distribution between ~200-600bp using AMPure XP beads (Beckman Coulter). ~ 2µg of size-selected DNA was used for library preparation using KAPA hyper prep kit (KAPA biosystems) and TruSeq DNA unique dual indexes (Illumina). The number of PCR cycle used for library amplification was determined by KAPA library quantification kit for Illumina platform (KAPA biosystems). Each Hi-C library was sequenced to obtain 500M reads PE100 with biological duplicates to achieve a total of 1 B reads for each condition.