Fig. 3: Epigenomic profiles of H3K27me3 and H3K4me3 scSET-seq are differently correlated with corresponding gene expressions.

a Joint views showing the IGV examples of aggregated epigenomic signals and violin plots of expression levels. Three marker genes, which were labeled red at the bottom, of each cluster were shown. The epigenomic signals were aggregated from cells of the indicated cluster. P values were calculated by Student’s t-test, two-sided. n = 83 (H3K4me3 Mix cluster), 75 (H3K4me3 Proxi cluster), 52 (H3K4me3 Dista cluster), 208 (H3K27me3 Mix cluster), 58 (H3K27me3 Proxi cluster), and 60 (H3K27me3 Dista cluster) cells *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001. Exact P values were provided in Supplementary Dataset 4. b Schema showing the process of co-embedding of epigenomic and transcriptional profiles from scSET-seq. See main text for description. c Heatmaps showing the co-embedded signals in single cells. Marker genes with both H3K27me3 and transcriptional signals were shown. To assign the H3K27me3 signals, peaks that were called from the aggregated data were preferably annotated to genes within 3 Kb from their transcription starting sites, then to the closest genes within 500 Kb. d Same as in c, except H3K4me3 scSET-seq data were plotted. Source data are provided as a Source Data file.