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bioRxiv · 10.1101/2020.04.27.064592

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

Chin, H. G.·Sun, Z.·Vishnu, U. S.·Hao, C.·Cejas, P.·Spracklin, G.·Esteve, P.-O.·Xu, S.-y.·Long, H. W.·Pradhan, S.
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Abstract

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 tissue sections. We also demonstrate one tube UniNicE-seq for FFPE tissue section for direct NGS library preparation without sonication and DNA purification steps. These refinements allowed reliable mapping of accessible chromatin for high resolution genomic feature studies.

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Chin, H. G., Sun, Z., Vishnu, U. S., Hao, C., Cejas, P., Spracklin, G., Esteve, P.-O., Xu, S.-y., Long, H. W., Pradhan, S.. 2020-04-29. Universal NicE-seq for high resolution accessible chromatin profiling for formaldehyde fixed and FFPE tissues. https://doi.org/10.1101/2020.04.27.064592

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