Extended Data Fig. 7: Single-incubated data from H3K4me1 and H3K9me3 builds a model for inferring cluster-pairs in double-incubated data.

(a) Heatmap of H3K4me1 signal across clusters for 811 cell type-specific regions (Methods). These regions come from cell type-specific genes used in Fig. 2e. (b) Heatmap of H3K9me3 signal across clusters for 6085 cluster-specific regions (50 kb genomic window). These regions come from the statistically significant dynamic regions of H3K9me3 defined in Extended Data Fig. 4a. (c) Schematic of how a cluster-pair is inferred from each double-incubated cell. Each double-incubated cell has a vector of counts across 6896 regions (811 regions come from H3K4me1, while 6085 come from H3K9me3). We calculate the log-likelihood (Methods) of the observed double-incubated cell counts for each cluster-pair (32 cluster-pairs from 8 clusters in H3K4me1 and 4 clusters in H3K9me3). From the 32 log-likelihood estimates, we assign the cell to the cluster-pair with the highest probability. (d) Examples of the 32 log-likelihood estimates from eight representative cells, shown as a 4-by-8 heatmap. Each of the four rows is a cluster from H3K9me3; each of the eight columns is a cluster from H3K4me1. (e) Histogram of the highest assignment probability per cell.