Universal NicE-seq for high resolution accessible chromatin profiling for native and formaldehyde fixed cells and tissues

Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negate the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen and FFPE tissue sections. These refinements allowed reliable mapping of accessible chromatin for high resolution genomic feature studies. Overall design: Open-chromatin profile of various samples from cultured cancer cell lines, mouse tissue and human tissue section using nicking enzyme, NtCviPII based NicE-seq library were generated and sequenced. Depending on the experiments some samples were sequenced once, in duplicate or triplicate.