{"entity": "publication", "iuid": "cf3c179176354f60b3454b5d80a14496", "timestamp": "2026-08-20T21:31:42.412Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cf3c179176354f60b3454b5d80a14496.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cf3c179176354f60b3454b5d80a14496"}}, "title": "FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers.", "authors": [{"family": "Zhao", "given": "Linxuan", "initials": "L", "orcid": "0000-0002-8883-5656", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7578093c7e0c4220a0035bc2ff7a482b.json"}}, {"family": "Xing", "given": "Pengwei", "initials": "P"}, {"family": "Polavarapu", "given": "Vamsi Krishna", "initials": "VK"}, {"family": "Zhao", "given": "Miao", "initials": "M"}, {"family": "Valero-Mart\u00ednez", "given": "Blanca", "initials": "B"}, {"family": "Dang", "given": "Yonglong", "initials": "Y"}, {"family": "Maturi", "given": "Nagaprathyusha", "initials": "N"}, {"family": "Mathot", "given": "Lucy", "initials": "L"}, {"family": "Neves", "given": "In\u00eas", "initials": "I"}, {"family": "Yildirim", "given": "Irem", "initials": "I"}, {"family": "Swartling", "given": "Fredrik Johansson", "initials": "FJ"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}, {"family": "Uhrbom", "given": "Lene", "initials": "L"}, {"family": "Chen", "given": "Xingqi", "initials": "X", "orcid": "0000-0002-5657-2839", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ffb9d3c94e54fac97be6c78586940eb.json"}}], "type": "journal article", "published": "2021-12-02", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "49", "issue": "21", "pages": "e125", "issn-l": "0305-1048"}, "abstract": "The majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10-20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7-pA-Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing \u223c4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease.", "doi": "10.1093/nar/gkab813", "pmid": "34534335", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8643707"}, {"db": "pii", "key": "6371973"}], "notes": [], "created": "2026-08-20T09:49:43.106Z", "modified": "2026-08-20T09:49:43.237Z"}