Extended Data Fig. 3: Single-cell multiome analyses identified transitioning individual cells with intermediate transcriptome and chromatin states.

a, PCA analyses of chromatin accessibility of LNCaP⁺FOXA2 cells, along with LuCaP PDX, Merkel cell carcinoma (MCC) and NEPC cell lines (NCI-H660 and EF1-CFCE) using differentially accessible peaks (n = 368,330) identified by DESeq2 (adjusted p < 0.05). Adjusted p values were calculated by a likelihood ratio test with Benjamini–Hochberg correction. b, Genome browser views of ATAC–seq signal at NE lineage genes (POU3F2 and NCAM1, top row) and luminal lineage genes (KLK3 and HOXB13, bottom row) in time-course LNCaP+FOXA2 cells. c, TF motifs were plotted by ranks generated from their associated differential p values at ATAC–seq peaks in D2 and D28 LNCaP⁺FOXA2 samples. P values by two-sided hypergeometric test with Benjamini–Hochberg correction. d, UMAP integration of D0, D14 and D21 LNCaP⁺FOXA2 cells with previously published clinical PCa cells. e, Pseudotime trajectories in PCa cells shown in d. Color reflects pseudotime distance (primary PCa located at time = 0). f, UMAP visualization of AR and AR target genes (KLK3, NKX3-1) and NE lineage genes (SYP, NCAM1, POU3F2) in D0, D14 and D21 LNCaP⁺FOXA2 scRNA-seq samples. Color bars: normalized expression.