Journal: bioRxiv

Article Title: CUT&Tag recovers up to half of ENCODE ChIP-seq peaks

doi: 10.1101/2022.03.30.486382

Figure Lengend Snippet: 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, optimisation 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.

Article Snippet: The following histone deacetylase inhibitors were used: Sodium butyrate (Merck B5887-250MG; used at 5 mM in CUT&Tag solutions with HDACi treatment), Trichostatin A (Enzo Life Sciences BML-GR309-0001; used at 1 μM in CUT&Tag solutions with HDACi treatment).

Techniques: DNA Extraction, Sequencing, Functional Assay