GSM8068229: CD34+-derived proE/basoE cells, MDS SF3B1 WT, rep NT 6; Homo sapiens; OTHER
8x10^6 cells were harvested and processed for genomic DNA extraction by SDS/ Proteinase K treatment at 37°C followed by phenol-chloroform extraction and ethanol precipitation. 8 µg of genomic DNA was fragmented using HindIII, EcoRI, BsrGI, XbaI, and SspI. Then DNA pre-treated or not with RNase H1 (16UI/mL) overnight (New Engl Biolabs, Ipswitch, MA) was immunoprecipitated using S9.6 antibody overnight at 4°C. For DRIP-seq, good quality DRIPed DNA samples (with and without RNase H1-treatment) were sonicated to get an average length 200-300 bp. Then samples were subjected to end-repair, dATP tailing, adaptor ligation and library indexing. Lastly, the libraries were cleaned up using AMPure beads, and amplified. After checking library quality on Agilent Bioanalyzer using Agilent High Sensitivity DNA 1000 kit, libraries were sequenced on Illumina NovaSeq instruments.