GSM5708359: MCF7-TWIST1 ChIP-Seq; Homo sapiens; ChIP-Seq
ChIP assays were performed using the SimpleChIP Enzymatic Chromatin IP Kit (Magnetic Beads) (9005S; Cell Signaling Technology) according to the manufacturer's instructions. Sample quality checks were performed by using the NanoDrop spectrophotometer, Invitrogen Qubit 2.0 DNA quantitation assay and Agilent Bioanalyzer. The Rubicon ThruPlex DNA-Seq library preparation system (p/n R400523, protocol QAM-328-001) was used to prepare ChIP-Seq libraries for sequencing on the Illumina NGS sequencing instruments. 1 ng of ChIP'd DNA was used for generating a double-stranded DNA library. The genomic DNA fragments were blunt ended and then the 5' end of the fragments were ligated with stem-loop adapters with blocked 5' end, leaving a nick at the 3' end. Then, the 3' end was extened during library synthesis and Illumina-compatible indexes were incorporated with 11 amplification cycles. The fragments were purified by using the AMPure XP Bead Purification System. Fragments with a size smaller than 200 bp as well as unincorporated PCR reagents and nucleotides were removed. The resulting libraries were quantitated by using the NanoDrop ND-1000 spectrophotometer and the fragment sizes were assessed with the Agilent Bioanalyzer. To determine the concentration of adapter ligated fragments, the libraries were quantitated by qPCR by using the Applied Biosystems ViiA7 TM Real-Time PCR System and a KAPA Library Quant Kit.