title: GSM8098669: Capture HiC, Zfp661 KO mESCs, replicate 1; Mus musculus; Hi-C
library_construction_protocol: Cells were crosslinked with 2% formaldehyde for 10 min and quenched using 0.4M glycine for 5 min. Cells with approximately 4 μg of DNA were used as input to generate proximally ligated DNA using the Arima-HiC kit (Arima, A510008) according to the manufacturer's protocol (Arima, A160134 v01). Briefly, crosslinked cells were digested using the Arima restriction enzyme cocktail, the 5' overhangs were filled in and labeled with a biotinylated nucleotide, and the spatially proximal ends were ligated. The proximally ligated DNAs were purified and sonicated using the Covaris ME220 (8 microTube-130 AFA fiber strip V2: duration 42s, peak power 70w, duty factor 20%, cycle per burst 1000#). Then, size selection was performed on the resulting DNA Fragments (for size ranging from 200 to 600 bp). 2 μg of the resulting DNA fragments were used as input, and fragments labelled with biotin were bound to beads to construct Hi-C libraries using the KAPA HyperPrep Kit (Roche, KK8502) following the protocol provided by Arima (A160139 v00). For Capture Hi-C, probes were designed to cover several regions bound by ZFP661 using the SureSelect DNA tool of Agilent SureDesign with the following settings: 2X tiling density, moderately stringent masking, and optimized performance for HS2/XT. The Capture Hi-C libraries were obtained by fast hybridization for 90 min with probes, followed by capture, washes and post-capture amplification using the SureSelect XT HS2 DNA Target Enrichment Kit (Agilent, G9987A) according to the protocol (Agilent, G9983-90000).