{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T03:42:34Z","timestamp":1790739754496,"version":"4.1.0"},"reference-count":26,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2022,8,22]],"date-time":"2022-08-22T00:00:00Z","timestamp":1661126400000},"content-version":"vor","delay-in-days":21,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2022,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>In basic and translational cancer research, the majority of biopsies are stored in formalin\u2010fixed paraffin\u2010embedded (FFPE) samples. Chromatin accessibility reflects the degree to which nuclear macromolecules can physically interact with chromatinized DNA and plays a key role in gene regulation in different physiological conditions. As such, the profiling of chromatin accessibility in archived FFPE tissue can be critical to understanding gene regulation in health and disease. Due to the high degree of DNA damage in FFPE samples, accurate mapping of chromatin accessibility in these specimens is extremely difficult. To address this issue, we recently established FFPE\u2010ATAC, a highly sensitive method based on T7\u2010Tn5\u2010mediated transposition followed by <jats:italic>in vitro<\/jats:italic> transcription (IVT), to generate high\u2010quality chromatin accessibility profiles with 500\u201350,000 nuclei from a single FFPE tissue section. In FFPE\u2010ATAC, which we describe here, the T7\u2010Tn5 adaptors are inserted into the genome after FFPE sample preparation and are unlikely to sustain the DNA breakage that occurs during reverse cross\u2010linking of these samples. It should, therefore, remain at the ends of broken accessible chromatin sites after reverse cross\u2010linking. IVT is then used to convert the two ends of the broken DNA fragments to RNA molecules before making sequencing libraries from the IVT RNAs and further decoding Tn5 adaptor insertion sites in the genome. Through this strategy, users can decode the flanking sequences of the accessible chromatin even if there are breaks between adjacent pairs of T7\u2010T5 adaptor insertion sites. This method is applicable to dissecting chromatin profiles of a small section of the tissue sample, characterizing stage and region\u2010specific gene regulation and disease\u2010associated chromatin regulation in FFPE tissues. \u00a9 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.<\/jats:p><jats:p><jats:bold>Basic Protocol 1<\/jats:bold>: Nuclei isolation from FFPE tissue samples<\/jats:p><jats:p><jats:bold>Basic Protocol 2<\/jats:bold>: T7\u2010Tn5 transposase tagmentation, reverse\u2010crosslinking, and <jats:italic>in vitro<\/jats:italic> transcription<\/jats:p><jats:p><jats:bold>Basic Protocol 3<\/jats:bold>: Preparation of libraries for high\u2010throughput sequencing<\/jats:p>","DOI":"10.1002\/cpz1.535","type":"journal-article","created":{"date-parts":[[2022,8,22]],"date-time":"2022-08-22T14:11:02Z","timestamp":1661177462000},"source":"Crossref","is-referenced-by-count":14,"title":["FFPE\u2010ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin\u2010Fixed Paraffin\u2010Embedded Samples"],"prefix":"10.1002","volume":"2","author":[{"given":"Ram Prakash","family":"Yadav","sequence":"first","affiliation":[{"name":"Department of Immunology, Genetics and Pathology Uppsala 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