One-pot universal NicE-seq: All enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics

Accessible chromatin landscape allows remodeling of transcription factors and enhancers during development and molecular subtypes of cancer in patient samples. One-tube universal NicE-seq (OuNicE-seq) is an improved accessible chromatin profiling method that negate DNA purification and incorporate sonication free enzymatic fragmentation before library preparation and is suited to a variety of mammalian cells. OuNicE-seq is versatile, capable of profiling 4% formaldehyde fixed chromatin in 25 fixed cells and opens the possibility for automation. Accessible chromatin profile is more efficient on formaldehyde fixed cells using OuNicE-seq compare to Tn5 transposon mediated methods, demonstrating its versatility. HCT116, HeLa, HEK293 and GM12878 cells were grown according to ATCC ‘s recommendations. DNA damage detection and chromatin labeling efficiency studies were performed in HCT116 with 0.2%, 1% and 4% formaldehyde fixation. OuNicE-seq for low cell numbers were performed in HCT116, HeLa, HEK293 and GM12878 cells fixed with 4% formaldehyde. Accessible chromatin labeling was done based on UniNicE-seq protocol and library for sequencing was generated based on OuNicE-seq protocol.