The potential impact of VHL on chromatin accessibility using the assay for ATAC-seq in Caki-1 cells.

To investigate the potential impact of VHL on chromatin accessibility, the assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) was performed in renal cell carcinoma cells.The VHL wild-type Caki-1 cells were used to generate control or VHL knockout cells by CRISPR/Cas9-mediated genome editing (sgCTR and sgVHL Caki-1 cells).Following ATAC-seq, DNAs were amplified using non-biased conditions, labeled, and sequenced with Illumina NovaSeq 6000. Overall design: The VHL wild-type Caki-1 cells were used to generate control or VHL knockout cells by CRISPR/Cas9-mediated genome editing (sgCTR and sgVHL Caki-1 cells). In sgCTR and sgVHL Caki-1 cells, nuclei were removed from samples and resuspended in the Tn5 transposase reaction mix. For 30 min, the transposition process was incubated at 37°C. After transposition, equimolar Adapter 1 and Adapter 2 were introduced, and the library was amplified using PCR. Libraries were purified using DNA clean beads after the PCR process, and library quality was evaluated with Qubit. The library preparations were sequenced on an Illumina NovaSeq 6000 platform after cluster creation, yielding 150 bp paired-end reads.