Optimized adapter:DNA ratios for efficient ChIP-seq library preparation from low input samples

The goal of this study was to titrate the amount of adapters for picogram amounts of ChIP DNA to determine the optimal conditions for library generation. H3K4me3 ChIP DNA from human Raji cells was diluted to the indicated amount and sequencing libraries generated using a range of adapter concentrations. The optimal adapter:DNA ratios were sequenced in technical duplicate to determine the reproducibility at each starting ChIP DNA amount. Additionally, for two samples we altered the number of cycles during the PCR amplification to determine the effect of PCR on library complexity and read duplicates. Overall design: H3K4me3 ChIP DNA from human Raji cells was diluted to the indicated amount and sequencing libraries generated using a range of adapter concentrations.