GSM8425103: HCT116_L1_Auxin_CaptureMicroC_Rep2; Homo sapiens; OTHER
Cells were aliquoted between 1.2 to 2 x 10⁶ cells in individual Eppendorf tubes. Aliquots were spun down and washed in PBS. The supernatant was carefully removed and discarded. Cell pellets were stored at -80°C for at least a day. Pre-freezing is required to get an optimal MNase digestion profile. Cell pellets were thawed at room temperature and then processed as prescribed by the Micro-C protocol (Dovetail). For the end repair steps, we used the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645) instead of the Dovetail kit. After adapter ligation with the NEB kit, DNA was purified via SPRI beads (Beckman A63880) as described in the Dovetail kit. Ligation capture and library amplification was performed with reagents from the Dovetail kit, except for the sequence index which was taken from the NEB kit. After verifying that libraries had a correct concentration and size distribution, we continued with the Agilent SureSelectXT HS2 Kit. Capture probe design was performed by Agilent. The coordinates of capture probes were: chr8:60,458,500-61,587,500 for L1 and No Loop loci, chr2:235,182,500-236,297,500 for L2 and chr1:36,700,000-38,175,000 for T1. . We sequenced with BGI Illumina 100-bp paired-end sequencing (PE100).