Arabidopsis thaliana Raw sequence reads
Chromatin immunoprecipitation and sequencing (ChIP-seq) is an essential tool for epigenetic and molecular genetic studies. Although being routinely used, ChIP-seq is expensive, requires grams of plant materials, and is challenging for samples that enrich secondary metabolites such as seeds.Here, we developed an Ultrasensitive Plant ChIP-seq (UP-ChIP) method based on native ChIP-seq combined with Tn5 tagmentation-based library construction strategy. UP-ChIP is generally applicable for profiling histone modification and Pol II in a wide range of plant samples such as a single Arabidopsis seedling, a few Arabidopsis seeds and sorted nuclei.Compared with conventional ChIP-seq, UP-ChIP is much less labor intensive and only consumes 1ug of antibody and 10ul of Protein A/G conjugated beads for each IP and can work effectively with the amount of starting material down to a few milligrams. By performing UP-ChIP in various conditions and genotypes, we showed that UP-ChIP is highly reliable, sensitive, and quantitative for studying histone modifications. Detailed UP-ChIP protocol is provided as well.We recommend UP-ChIP as an alternative to traditional ChIP-seq for profiling histone modifications and Pol II, offering the advantages of reduced labor intensity, decreased costs, and minimal sample input.