ATAC-seq library preparation and sequencing

For each PDPCO line, we prepared two sequencing libraries (technical replicates). PDPCOs in Matrigel were collected and washed with precooled PBS. Cells were washed once with 200 μl of cold PBS buffer and were then centrifuged for 5 min at 500× g and 4 °C. The supernatant was removed and discarded. The cell pellet was resuspended in 50 μl of cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) by gently pipetting up and down. The cells were immediately centrifuged at 500Xg for 5 min at 4 °C to collect nuclei, and the transposition reaction was immediately continued. ATAC-seq libraries were generated using a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on the Illumina Nova platform, and 150 bp paired-end reads were generated. Libraries that contained less than 15 million aligned, deduplicated reads were sequenced again, and the additional reads were pooled prior to deduplication.