GSM8670968: Monocyte,HiC, rep2; Homo sapiens; Hi-C
In situ Hi-C in monocytes and HL60 cells was performed using the Arima HiC kit (Arima Genomics), following the user guide for mammalian cell lines. For the crosslinking step, according to the standard input protocol, 5 million cells were crosslinked then flash-frozen in aliquots of 1 million cells. After estimating the DNA input from crosslinked cells, one aliquot of cells (~2 ug of DNA) per condition was sufficient to proceed with the Hi-C protocol. Digestion and proximity ligation steps were done according to the kit protocol. Proximally ligated DNA underwent quality control checks for ligation, sonicated with the Covaris ME220 sonicator, then purified and size selected with AMPure XP Beads (Beckman Coulter) to obtain a fragment size distribution of 200-600bp prior to the biotin enrichment step. For library preparation, end repair, dA-tailing, and adaptor ligation were performed using the NEB Next Ultra II DNA Library Prep kit for Illumina, following a protocol tailored for Arima Hi-C DNA. The Hi-C libraries were sequenced at a depth of at least 300 million 50bp paired-end reads on the Illumina NextSeq 500 Sequencer.