GSM8224471: Breast_tumor_HiC; Homo sapiens; Hi-C
Breast tissue was acquired from three Tru-Cut biopsies. The tissue was sectioned into small fragments and cryopreserved in FBS (Gibco) supplemented with 10% dimethyl sulfoxide (DMSO, Sigma). Upon thawing, the tissue was enzymatically dissociated using Accumax solution (Sigma) and incubated for 30 minutes. The resulting cell suspension was filtered through a 40 µm filter, followed by processing using the Dead Cell Removal Kit (Miltenyi Biotec #130090101) through two rounds to ensure sufficient viability. Cells were cross-linked with 2% formaldehyde. Then cell nuclei were obtained with a lysis buffer (10 mM Tris-HCl pH 8, 0.2% IGEPAL CA-630, 10 mM NaCl, 1X cOmpleteR protease inhibitors cocktail). For genome digestion, 125 U of DpnII (New England Biolabs) were added. The ligation spet was performed using 50 U Weiss of T4 DNA Ligase enzyme (Thermo Scientific, 5 U Weiss/μl), and the crosslink was reversed. DNA was purified using a Phenol-Chloroform-Isoamyl alcohol mix (25:24:1) and shared with a Covaris Sonicator. Hi-C libraries were generated using the TruSeq Illumina system.