GSM8342826: ATAC_H1975_shCtrl; Homo sapiens; ATAC-seq
ATAC-seq libraries were prepared according to the ATAC-seq kit (Diagenode; #C01080001) protocol. The ATAC-seq assay was conducted following the optimized Diagenode protocol. Initially, cells were processed by pelleting, lysing, washing, and re-pelleting using the specified lysis and wash buffers. Subsequently, a transposition mix containing Tn5 was added to the samples, and the transposition reaction was carried out at 37 °C for 30 minutes in a thermomixer set at 1000 rpm. Following transposition, the transposed DNA was purified using the QIAquick PCR Purification Kit (QIAGEN, Germany). PCR was performed to amplify the library for 12 cycles using the following PCR conditions: 72°C for 3 min, 98 °C for 30 s, and thermocycling at 98°C for 15 s, 60 °C for 30 s, and 72°C for 3 min; following by 72°C 5 min. Libraries were purified with AMPURE XP Bead-based reagent to remove contaminating primer dimers. Library quality was checked using Qubit 2.0 Fluorimeter (Invitrogen, United States). Lastly, the samples were subjected to paired-end 75-bp sequencing on an Illumina Novaseq 6000.