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CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

ABSTRACT: CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

PROVIDER: PRJNA1209791 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31972716_1.fastq.gz	Fastqsanger.gz
	SRR31972716_2.fastq.gz	Fastqsanger.gz
	SRR31972717_1.fastq.gz	Fastqsanger.gz
	SRR31972717_2.fastq.gz	Fastqsanger.gz
	SRR31972718_1.fastq.gz	Fastqsanger.gz

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

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

Project description:We comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Across a total of 30 new and 6 published CUT&Tag datasets we found that no experiment recovers more than 50% of known ENCODE peaks, regardless of the histone mark. We tested peak callers MACS2 and SEACR, identifying optimal peak calling parameters. Balancing both precision and recall of known ENCODE peaks, SEACR without retention of duplicates showed the best performance. 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 and will facilitate future efforts to apply CUT&Tag in human tissues and single cells.

2022-03-31 | GSE199611 | GEO

CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks

Project 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.

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ChIP-seq. analysis of pan-histone 3 acetylation in Romidepsin treated TCam-2

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