Fig. 2

Comparison of AutoCUT&RUN versus ENCODE ChIP-seq. a A representative silenced domain flanked by active genes is shown for human K562 cells probed using the same antibodies by either AutoCUT&RUN or ChIP-seq. For each comparison, ChIP-seq tracks are shown that include either all sequenced fragments or the same number of sampled fragments as the AutoCUT&RUN data. b Heat map comparison of H3K4me1 Ab8895 ± 1 kb around peak centers (summits) called by MACS2 for AutoCUT&RUN data and for ENCODE ChIP-seq data (broad peaks by Broad Institute and narrow peaks by SYDH). Signal intensities reflect the relative number of reads that fall within peaks. c Correlation matrix comparing batches (B) and replicates (R) between AutoCUT&RUN and ENCODE ChIP-seq datasets for H3K4me1 Ab8895