Fig. 1: Overview of experimental design and computational benchmarking.
From: CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks
a Summary of experimental design. Five antibodies were tested at dilutions 1:50, 1:100, and 1:200, and 11, 13, or 15 PCR cycles for library preparation. H3K27ac libraries were assessed with and without HDAC inhibitor Trichostatin A (TSA; 1 µM) or sodium butyrate (NaB; 5 mM). Column- and SDS-based DNA extraction methods were compared. Antibody performance was assessed by qPCR and sequencing, and sequenced reads were processed with and without duplicates using peak callers SEACR and MACS2. b Summary of analytical approaches. Analysis comprised quality control of sequencing data, optimization of peak calling approaches with both peak callers, and comparison between CUT&Tag and ENCODE datasets at the level of reads, peaks, and functional annotation.
