GSM8254283: DLD-1 cells, sgGATA6, HiC; Homo sapiens; Hi-C
In situ Hi-C experiments were performed following the previously described protocol (Rao et al., 2014) with modifications. Briefly, chromatin extracted from crosslinked cells was digested with restriction enzymes, followed by biotin labeling, ligation, and biotin pull down. HiChIP experiments were performed using Arima HiC+ kit following manufacture's protocol with modifications. Briefly, 10 million cells were crosslinked with 2% formaldehyde (Millipore Sigma, 252549), followed by cell lysis, restriction enzyme digestion, end repair and biotin labeling, ligation, and shearing following Arima Hi-C procedure. Chromatin was then subjected to immunoprecipitation with H3K27ac antibody (active motif, 39133) ChIA-PET data was generated following the previously described ChIA-PET protocol 3, 4. Antibody against GATA6 (CST, 5851) was used. The final library was sequenced as 150 PE reads on Illumina Novaseq 6000 platform. The final library was prepared using the KAPA HyperPrep kit (KAPA, 7962363001). The final library was sequenced as 150 PE reads on Illumina Novaseq 6000 platform.