GSM9675391: Vector control, biological replicate 1; Homo sapiens; ATAC-seq
Approximately 5 × 10^4 HCCLM3 cells were collected and washed once with cold 1× PBS, followed by centrifugation at 500 × g for 5 min at 4°C. Cell pellets were resuspended in 50 μl pre-chilled nuclei lysis buffer and gently pipetted to release nuclei. Nuclei were collected by centrifugation at 500 × g for 10 min at 4°C, and the supernatant was discarded immediately before transposition. ATAC-seq libraries were prepared from isolated nuclei using Tn5 transposase. Nuclei were resuspended in transposition reaction mix and incubated at 37°C for 30 min. Transposed DNA was purified using the Qiagen MinElute PCR Purification Kit. Libraries were amplified by PCR using NEBNext High-Fidelity 2× PCR Master Mix for 10–15 cycles and purified again using the Qiagen MinElute PCR Purification Kit. Library concentration was measured using Qubit 4.0, and fragment size distribution was assessed using QSep400. Qualified libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads.