The CUT&RUN suspect list of problematic regions of the genome.

ABSTRACT:

Background

Cleavage 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.

Results

We compile suspect lists based on CUT&RUN data for the human and mouse genomes, identifying regions consistently called as

SUBMITTER: Nordin A 

PROVIDER: S-EPMC10416431 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature