Fig. 1

Generation of the CUT&RUN suspect lists. A Schematic representation of suspect list generation strategy. B Plots of Spearman’s correlation between negative control samples (N = 20 each) in human and mouse, showing genome-wide correlation and correlation within the C&R suspect list regions in hg38 and mm10 genomes. In both human and mouse, samples show dramatically increased correlation when considering only the suspect list regions. The mouse dataset (15) that does not correlate well with the rest can be explained by an unequal distribution of reads among the chromosomes, with high enrichment for chromosome 1. C Signal enrichment plots of the hg38 suspect list regions for a representative human negative control sample, after mapping with bowtie or bowtie2. More stringent mapping with bowtie did not drastically change the enrichment in the suspect listed regions. D Chromosome map showing genome wide locations of regions contained in the C&R hg38 suspect list (left) and corresponding genomic annotations by HOMER (right). The hg38 suspect list is enriched for satellite and simple repeat regions. E Chromosome map showing the genome wide location of regions contained in the C&R mm10 suspect list (left) and corresponding genomic annotations (right). The mm10 suspect list contains many different types of regions, the most represented being intergenic loci