Extended Data Fig. 4: CoTECH Data quality and relationship between H3K4me3 and RNA in mESCs.
a, Hierarchical clustering of DNA profiles of different groups by using the genome-wide signals in non-overlapping 5-kb windows. b, Pearson correlation of gene expression (n=24,413 genes) between four CoTECH assays. Aggregated transcript reads were log10 normalized. Two-sided correlation coefficients, p value < 2.2e-16. c, Comparison of CoTECH assays with respect to mapping rate and exonic rate (n = 3,907 and 3,086 cells for CoTECH-RNA (H3K4me3) and CoTECH-RNA (H3K27me3), respectively). The boxes in violin plots indicate upper and lower quartiles (25th and 75th percentiles). d, Dimensionality reduction for visualizing 6,993 single cells (both DNA and RNA detected) from different replicates in mESCs using UMAP. e, UMAP showing cellular heterogeneity of individual cells using CoTECH-H3K4me3 profiles colored by different replicates of mESCs and NIH 3T3. f-g, Cell-normalized topic scores of specific topics for NIH 3T3 (f) and mESCs (g) identified by cisTopic using CoTECH-H3K4me3 data. The colors from grey to red indicate the topic scores from low to high. h, GO terms enriched in the NIH 3T3- and mESC-specific topic corresponding to (f) and (g). Top 5 terms of biological process were shown. P value was calculated by two-sided binomial test. Gene Ontology (GO) term enrichment analysis of each module was performed by GREAT. i, Heatmap showing the expression of feature genes in mESCs. Color bars indicate identified clusters (top row) as in Fig. 3b. The columns represent single cells ordered by pseudotime. j, Analytic strategy for examining H3K4me3-RNA concordance in a varying number of clusters of mESCs along pseudotime. k, Fraction of cells with concordance of RNA-H3K4me3 in a varying number of clusters of mESCs along pseudotime. l-m, Pseudotime of 6,993 single cells by monocle 2. Cells are colored by clusters (l) as in Fig. 3b and pseudotime (m). n, Heatmaps showing the normalized H3K4me3 signals (left) and gene expression (right) of genes upon changes in H3K4me3 signal across 3,907 mESCs. The columns represent single cells ordered by pseudotime. o, Scatter plot showing the pseudotime defined by H3K4me3 and RNA profiles for the same cells of mESCs. The scatters were fitted by locally weighted regression to a red curve.
