GSM5067589: PC3_ecDNA_positive-PolII-ChIA-Drop_rep2; Homo sapiens; OTHER
2 million cells were crosslinked, permeabilized and digested following the ChIA-PET protocol except the HindIII enzyme (R0104M, NEB) was used instead of AluI. The digested nuclei were collected for chromatin sonication followed by immunoprecipitation with anti-RNAPII antibody (920102, Biolegend). RNAPII-enriched chromatin was collected with EB Buffer and cleared through the Amicon Ultra-0.5 100 K column (Z740183-96EA, MilliporeSigma) following the manufacture's instruction to remove small fragments. The RNAPII-associated chromatin complexes were adjusted to a concentration of 0.5 ng/μl and proceeded to ChIA-Drop library construction using Chromium Genome v2 Library Kit & Gel Bead Kit (PN-120258, 10X Genomics) following the manufacturer's protocol. The final libraries were sequenced on Illumina platform with 150 bp pair-end sequencing.