Fig. 1: Dam&ChIC design and mapping of diverse chromatin feature combinations in single cells.
a, Graphical overview of the single-cell Dam&ChIC method. b, Violin plots depicting the unique number of reads obtained per cell by Dam&ChIC for different combinations of Dam constructs and antibodies. Violins show a kernel density estimation of the distribution of data points. c, Single-cell heatmaps of each chromatin feature profiled with Dam&ChIC. In silico bulk profiles are shown as OE values. Corresponding in silico bulk profiles of ChIC-only datasets in KBM7 cells are shown for comparison. For the untethered Dam, the in silico bulk of a corresponding publicly available DamID-only dataset in KBM7 cells20 is used for comparison. d, Heatmaps showing chromatin features profiled with Dam&ChIC aligned on KBM7 expressed genes. Genes (rows) are ordered on their relative expression levels, determined by publicly available RNA-seq data29. Line plots indicate scaled averages of the heatmaps for each mapped chromatin feature. e, Hierarchical clustering depicting genome-wide Pearson correlations relating all in silico bulk Dam&ChIC chromatin data and corresponding ChIC-only datasets, or a publicly available DamID-only dataset29. Data were binned in 1-kb bins. Data labelled as ‘Dam’ or ‘Dam–LMNB1’ (Dam&ChIC colour label), contain the respective DamID readouts from all experimental combinations with hPTMs. f, UMAP representations of Dam&ChIC data binned in 100-kb genomic bins. Each cell (dot) is represented twice, once for each measurement. Left; coloured by chromatin target, right; coloured by experimental combination. Black lines in the left UMAP connect the same cell. Source numerical data are available in source data.
