Fig. 3: Single-cell multiome identified transitioning individual cells with intermediate transcriptome and chromatin states.
a, K-means clustering reveals six clusters of differential ATAC–seq peaks (±2 kb) across time-course LNCaP+FOXA2 samples (adjusted P < 0.0001). Heatmaps shown here were scaled across samples. Significantly enriched TF motifs and GO terms for each cluster, along with the number of peaks, are shown on the right. Color bar at the bottom indicates the scale of enrichment intensity. Adjusted P values were calculated using the likelihood ratio test followed by Benjamini–Hochberg correction. b, Genomic distribution of the six clusters of ATAC–seq peaks in a. c–f, scRNA-seq UMAP visualization of D0, D14 and D21 LNCaP+FOXA2 cells (c), AR (d) and NE (e) signature genes, which are further quantified for the proportion of AR+/ARS+, AR+/ARS−, AR−/NES− and AR−/NES+ cells (f). g, RNA velocity analysis of D14 LNCaP+FOXA2 cells. The data are visualized as streamlines in a UMAP-based embedding. Blue dots indicate KLK3-high cells, and the yellow dots indicate KLK3-low cells. h–j, scATAC–seq UMAP visualization of D0, D14 and D21 LNCaP+FOXA2 cells (h), chromatin accessibility (i) and expression (j) of ARS/NES genes. Red and green arrows indicate transitioning D14 and D21 cells, respectively. enhs, enhancers.
