sci-ATAC-seq identifies unique neuronal adhesion molecules and common transcription factor networks in high-grade localized prostate cancers

Flash-frozen prostate tumors collected from patients via radical prostatectomy were analyzed using single-cell ATAC-seq (sci-ATAC-seq). Unique cis- and trans-regulatory signatures between low- and high-grade localized prostate tumors are uncovered. Nuclei was extracted from frozen prostate tumors using a dounce homogenizer. FFPE blocks were cretaed with the rest of the tumor for tissue sectioning. Extracted nuclei were tagmented with barcoded transposomes using a 96-well plate. A secondary set of barcodes were introduced after the tagmentation reaction via PCR. As a result of this two-step barcoding, individual nuclei acquire a unique set of indeces in a high-throughput way.