Extended Data Figure 9. Location of CENP-A chromatin within the CHM13 D8Z2 α-satellite HOR array.

a,b) Plot of a) the ratio CENP-A ChIP to bulk nucleosome reads mapped via BWA-MEM, or b) the number of k-mer-mapped CENP-A ChIP (black) or bulk nucleosome (dark gray) reads (Methods). Shown are two independent replicates of CENP-A ChIP-seq performed on CHM13 cells (top two panels), as well as single replicates of CENP-A ChIP-seq performed on human diploid neocentromeric cell lines (bottom two panels; Methods). While the neocentromeric cell lines have a neocentromere located on either chromosome 13 (IMS13q) or 8 (MS4221)^24,25, they both have at least one karyotypically normal chromosome 8 from which centromeric chromatin can be mapped. We limited our analysis to diploid cell lines rather than aneuploid ones to avoid potentially confounding results stemming from multiple chromosome 8 copies that vary in structure, such as those observed in HeLa cells⁸⁷.