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The CUT & RUN suspe...
The CUT & RUN suspect list of problematic regions of the genome
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- Nordin, Anna (författare)
- Linköpings universitet,Avdelningen för molekylär medicin och virologi,Medicinska fakulteten,Wallenberg Centre for Molecular Medicine
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- Zambanini, Gianluca (författare)
- Linköpings universitet,Avdelningen för molekylär medicin och virologi,Medicinska fakulteten,Wallenberg Centre for Molecular Medicine
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- Pagella, Pierfrancesco (författare)
- Linköpings universitet,Avdelningen för molekylär medicin och virologi,Medicinska fakulteten,Wallenberg Centre for Molecular Medicine
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- Cantù, Claudio (författare)
- Linköpings universitet,Avdelningen för molekylär medicin och virologi,Medicinska fakulteten,Wallenberg Centre for Molecular Medicine
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(creator_code:org_t)
- BMC, 2023
- 2023
- Engelska.
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Ingår i: Genome Biology. - : BMC. - 1465-6906 .- 1474-760X. ; 24:1
- Relaterad länk:
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https://liu.diva-por... (primary) (Raw object)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- BackgroundCleavage Under Targets and Release Using Nuclease (CUT & RUN) is an increasingly popular technique to map genome-wide binding profiles of histone modifications, transcription factors, and co-factors. The ENCODE project and others have compiled blacklists for ChIP-seq which have been widely adopted: these lists contain regions of high and unstructured signal, regardless of cell type or protein target, indicating that these are false positives. While CUT & RUN obtains similar results to ChIP-seq, its biochemistry and subsequent data analyses are different. We found that this results in a CUT & RUN-specific set of undesired high-signal regions.ResultsWe compile suspect lists based on CUT & RUN data for the human and mouse genomes, identifying regions consistently called as peaks in negative controls. Using published CUT & RUN data from our and other labs, we show that the CUT & RUN suspect regions can persist even when peak calling is performed with SEACR or MACS2 against a negative control and after ENCODE blacklist removal. Moreover, we experimentally validate the CUT & RUN suspect lists by performing reiterative negative control experiments in which no specific protein is targeted, showing that they capture more than 80% of the peaks identified.ConclusionsWe propose that removing these problematic regions can substantially improve peak calling in CUT & RUN experiments, resulting in more reliable datasets.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Farmakologi och toxikologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Pharmacology and Toxicology (hsv//eng)
Nyckelord
- CUT & RUN; Chromatin; Bioinformatics; Peak calling; Blacklist; Suspect list
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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