GSM9385096: ATAC_G7883_resistant_MSTO_cells_rep1; Homo sapiens; ATAC-seq
Raw data were processed with the ENCODE ATAC-seq pipeline (v2.2.2) under default settings61. Adapters were trimmed with cutadapt (v2.5)62 , reads were aligned to hg38 with Bowtie2 (v2.3.4.3)63, and alignments were filtered for mapping quality and duplicates using samtools (v1.9)64 and Picard (v2.20.7) (Broad Institute). Peaks were called with MACS2 (v2.2.4) using Tn5 offset correction and smoothing65, and hg38 ENCODE blacklist regions were removed66 . Reproducibility was assessed with IDR (v2.0.4.2)67, and standard QC included mapping statistics, library complexity, replicate concordance, and TSS enrichment.