Single-cell assay for transposase-accessible chromatin sequencing of human clear cell renal cell carcinoma

Regulating the occurrence and progression of tumor cells at the epigenetic level is a new insight of clear cell renal cell carcinoma (ccRCC). Chromatin accessibility is an important pathway of epigenetic regulation, which may explain the mystery of tumor occurrence. Assay for transposase-accessible chromatin sequencing (ATAC-seq) provides insight into the epigenetic regulatory features of ccRCC, especially at the single-cell level. In this study, we performed scATAC-seq of 3 ccRCC samples and captured a total of 18,703 high-quality cell nuclei and 104,818 unique peaks. Our protocol for nuclear extraction was reliable and stable, which can be used to deal with fresh and frozen single-cell suspensions. We presented basic methods for scATAC-seq data analysis, such as cell clustering, gene activity scoring, cell subtype specific peaks, transcription factors, motif and motif footprinting analysis. Taken together, our data indicated the valuable epigenetic features of ccRCC, which will provide more references for the study of ccRCC.