Extended Data Fig. 5: Cross-target analysis in scMulTI-Tag.

a) Violin plots describing distributions of unique reads per cell in H1 cells (left) or K562 cells (right) for experiments described in Fig. 3. Median total unique reads (black), H3K27me3 unique reads (red), H3K4me2 unique reads (purple), or H3K36me3 unique reads (teal) are displayed at the top of each violin. Number of cells described is displayed at top of each cell type group. b) Heatmaps describing the enrichment of H3K27me3 (red), H3K4me2 (purple), or H3K36me3 (teal) signal from K562 cell profiles using single antibodies in bulk MulTI-Tag (left) or three antibodies sequentially in aggregate single cell MulTI-Tag (right) in H3K27me3 (top), H3K4me2 (middle), or H3K36me3 (bottom) peaks as called from bulk MulTI-Tag data. c) Heatmaps describing the same as b) for H1 hESCs. d) Violin plots describing the distribution of the fraction of on-target reads in peaks, defined as the percentage of reads corresponding to the same target for which the ENCODE ChIP-seq peak was called, in H3K27me3 (red, n = 74079), H3K4me2 (purple, n = 65388), and H3K36me3 (teal, n = 93085) peaks from bulk individual MulTI-Tag (white) vs. sequential single cell MulTI-Tag (grey) in K562 cells. e) Violin plots describing the same as d) for H1 hESCs (H3K27me3 n = 39290, H3K4me2 n = 119250, H3K36me3 n = 198078). f) Violin plots describing the distributions of proportions of each co-occurrence state as described below the plot in individual H1 (fuschia, n = 373) or K562 (gold, n = 372) cells, with points denoting individual cell values. The last four co-occurrence states are rescaled and inset at top right; p-values derived from two-sided student’s t-test comparing distributions between cell types are listed above violins (not corrected for multiple hypothesis testing).