title: GSM6253233: Input DMSO; Mus musculus; ChIP-Seq
library_construction_protocol: Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated. ChIP samples were purified using Agencourt AMPure XP beads and quantified with the Qubit. ChIP-seq libraries were prepared from 1.5-10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.