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. Overall design: 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.