In situ Hi-C seq of Oryzias latipes: Hd-rR embryonic fibroblast replicate1
In situ Hi-C was performed as previously described (Rao et al. 2014, Cell) with slight modifications. Samples (~2x10^6 cells of fibroblast or liver/brain from single individuals) were fixed with 1% (v/v) formaldehyde solution. MboI restriction enzyme (NEB) was used for digestion of cross-linked chromatin. After DNA shearing using the S220 Focused-ultrasonicator (Covaris), 300-500bp fragments were selected using AMPure XP beads (Beckman Coulter). End-repair, adapter ligation and library amplification were performed using KAPA Hyper Prep Kit (KAPA BIOSYSTEMS). Libraries were sequenced for 101 cycles from both ends on Illumina HiSeq 1500. Reads which were mapped around centromere was collected.