GSM8690825: 23935X15_ASPC1_sgNC_H3K27ac_rep1; Homo sapiens; OTHER
For HiChIP, 6 million cells were collected per replicate. Cells were fixed in 1% formaldehyde for 10min, then quenched with glycine to a final concentration of 125 mM. HiChIP protocol based on Mumbach et al., 2016, Nature Methods. Cross-linked chromatin was digested with the MboI restriction enzyme followed by end-repair with dNTPs including biotin labeled dATP, ligation using T4 DNA ligase, and sonication to obtain 1kb chromatin fragments using Qsonica (Q800). To enrich for chromatin interactions occurring at active regulatory elements, an anti-H3K27ac antibody (Abcam, ab4729, rabbit polyclonal, 7.5ug/HiChIP) was used for DNA fragment capture. Streptavidin magnetic beads were used to pull down ligated DNA fragments and HiChIP libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Kit. Sequencing was performed with the Illumina Nextera Library preparation.