Version: 1.0.0 | Published: 15 Oct 2026 | Updated: 0 days ago
Documentation
Description:
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. To optimize data analysis steps, we tested peak callers MACS2 and SEACR and identified optimal peak calling parameters. Considering both precision and recall of known ENCODE peaks, the peak callers were comparable in their performance, although peaks produced by MACS2 match ENCODE peak width distributions more closely. We found that reducing PCR cycles during library preparation lowered duplication rates at the expense of ENCODE peak recovery. Despite the moderate ENCODE peak recovery, peaks identified by CUT&Tag represent the strongest ENCODE peaks and show the same functional and biological enrichments as ChIP-seq peaks identified by ENCODE. Our workflow systematically evaluates the merits of methodological adjustments, providing a benchmarking framework for the experimental design and analysis of CUT&Tag studies, and will facilitate future efforts to apply CUT&Tag in human tissues and single cells
Overall design: 8 CUT&Tag experiments profiling H3K27ac and H3K27me3 in the K652 cell line using different antibodies (H3K27ac: Abcam ab177178, Abcam 4729, Diagenode C15410196, and H3K27me3: CST9733).
Coverage
Spatial:
US
Follow Up:
Unknown
Provenance
Temporal
Accrual Periodicity:
Static
Start Date:
01 January 2026
Time Lag:
Not applicable
Accessibility
Access
Access Rights:
See dataset for details. Access data at:
Usage
Resource Creators:
Sarah J Marzi
Observations
Statistical Population
Population Description
Population Size
Measured Property
Observation Date
Persons
1
Count
01 January 2026