RCC76
Here, two single-cell samples of ccRCC (ID: ccRCC 61 and ccRCC 76) were selected for bulk ATAC sequencing. A total of 10,000 cells were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% digitonin and 1% BSA) for 4 min on ice to isolate the nuclei. To perform Tn5 transposition, the nuclei collected by centrifugation for 500 g for 5 min at 4 C were incubated with the reaction mix (10 L of 5TTBL, 5 L of TTE Mix V50, 35 L of ddH2O) (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme, TD501-01) at 37 C for 30 min. After using 2 VAHTS DNA Clean Beads (Vazyme, N411) for purification, the DNA was added in the TruePrep Index Kit V2 for Illumina (Vazyme, TD202) and then amplified by PCR using the following PCR conditions (72 C for 3 min; 98 C for 30 s; and 15 cycles at 98 C for 15 s, 60 C for 30 s and 72 C for 30 s; 72 C 5min; 4 C hold). Finally, DNA libraries were purified with the 1.2 VAHTS DNA Clean beads and subjected to sequencing (Illumina NovaSeq 6000). For the raw data obtained by sequencing, samtools (version, 1.10) software was used to calculate the sequencing depth, coverage, alignment rate, repetition rate, etc. This process generated the .bam files. Then, we converted the .bam files to .bed files by using bedtools (version, 2.27.1) software. The bamCoverage (version, 3.1.1) software was used to convert .bam files into .bw files, which could be visualised by IGV (version, 2.11.9) software.