ChIP-seq library preparation comparative study

ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. To facilitate analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low DNA input amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. In this study, seven methods designed for low-input DNA/ ChIP-seq sample preparation (Accel-NGS 2S, Bowman-method, HTML-PCR, SeqPlex, DNA SMART, TELP and ThruPLEX) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material and compared to a gold standard PCR-free dataset. The performance of each method was examined for the prevalence of un-mappable reads, amplification-derived duplicate reads, reproducibility, and for sensitivity and specificity of peak calling.