This video is about ASHG Workshop - Pt2
Chromatin Immunoprecipitation sequencing (ChIP-seq) is routinely used to map covalent histone modifications and transcription binding sites. Typically, 1 ng or more of post-ChIP DNA is required to generate a sequencing library. However, as the analysis of epigenomes transitions from cell culture to primary cells and tissues, the amount of post-ChIP DNA is often in the picogram range. To address this technical limitation, a range of adapter:DNA molar ratios were titrated to optimize library preparation for 1 ng, 100 pg, and 10 pg of ChIP DNA using the KAPA Biosystems Hyper Prep Kit. The well-defined epigenetic modification H3K4me3 was used for the ChIP assay due to its localization to transcription start sites, thus providing a useful QC metric for non-specific enrichment. Optimal adapter concentrations were identified that maximized conversion efficiency and library yield while minimizing adapter dimer carry over. Sequencing of ChIP-seq libraries for each input DNA amount identified a highly significant overlap between libraries prepared from 1 ng, 100 pg and 10 pg of ChIP DNA. The 10 pg libraries were the most variable between technical replicates and identified fewer overall peaks, indicating an increase in the false-negative rate with lower input amounts. These data provide a technical resource for the generation of ChIP-seq libraries from picogram amounts of DNA and highlight limitations to interpretation of these data sets.