Profiling the epigenome at home

Steven Henikoff; Jorja G. Henikoff

We have developed a streamlined version of CUT&Tag that eliminates DNA extraction, so that all steps can be performed in a single PCR tube (Kaya-Okur et al., 2020) . CUT&Tag@home uses the same protocol, which allowed for a direct comparison of inlab to at-home implementation. To ascertain the ability of this CUT&Tag direct-to-PCR protocol to produce DNA sequencing libraries in our home laundry/utility room, we used frozen aliquots of native human K562 cell nuclei prepared in the laboratory and profiled there using the streamlined single-tube protocol. Aliquots of nuclei were thawed and serially diluted in Wash buffer from ~60,000 down to ~60 starting cells, where the average yield of nuclei was ~50%. We used antibodies to H3K27me3, which marks nucleosomes within broad domains of Polycomb-dependent silencing, and H3K4me3, which preferentially marks nucleosomes immediately downstream of active promoters. Aliquots of nuclei were taken home and stored in our kitchen freezer, then thawed and diluted at home, and profiled for H3K27me3 and H3K4me3. In both the laboratory and at home we performed all steps in groups of 16 or 32 samples over the course of a single day, treating all samples the same regardless of cell numbers. Whether produced at home or in the . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.15.043083 doi: bioRxiv preprint lab, all final barcoded sample libraries underwent the same quality control, equimolar pooling, and final SPRI bead clean-up steps in the laboratory prior to DNA sequencing. A total of 160 CUT&Tag@home libraries were sequenced by the Fred Hutch Genomics Shared Resource on three two-lane PE25 Illumina flow-cells runs for an estimated cost of ~$50 per sample for materials and sequencing.