{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Abbasova L"],"funding":["Medical Research Council","Alzheimer's Association"],"pagination":["2993"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11950320"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["16(1)"],"pubmed_abstract":["DNA-protein interactions have traditionally been profiled via chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). Cleavage Under Targets & Tagmentation (CUT&Tag) is a rapidly expanding technique that enables the profiling of such interactions in situ at high sensitivity. However, thorough evaluation and benchmarking against established ChIP-seq datasets are lacking. Here, we comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Combining multiple new and published CUT&Tag datasets, there was an average recall of 54% known ENCODE peaks for both histone modifications. We tested peak callers MACS2 and SEACR and identified optimal peak calling parameters. Overall, peaks identified by CUT&Tag repr"],"journal":["Nature communications"],"pubmed_title":["CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks."],"pmcid":["PMC11950320"],"funding_grant_id":["ADSF-21-829660-C","MR/W004984/1"],"pubmed_authors":["Ismail JN","Hu D","Skene NG","Abbasova L","Schilder BM","Urbanaviciute P","Marzi SJ","Nott A"],"additional_accession":[]},"is_claimable":false,"name":"CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks.","description":"DNA-protein interactions have traditionally been profiled via chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). Cleavage Under Targets & Tagmentation (CUT&Tag) is a rapidly expanding technique that enables the profiling of such interactions in situ at high sensitivity. However, thorough evaluation and benchmarking against established ChIP-seq datasets are lacking. Here, we comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Combining multiple new and published CUT&Tag datasets, there was an average recall of 54% known ENCODE peaks for both histone modifications. We tested peak callers MACS2 and SEACR and identified optimal peak calling parameters. Overall, peaks identified by CUT&Tag repr","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Mar","modification":"2026-06-02T06:35:07.84Z","creation":"2026-04-15T03:15:32.414Z"},"accession":"S-EPMC11950320","cross_references":{"pubmed":["40148272"],"doi":["10.1038/s41467-025-58137-2"]}}