ATAC-seq analysis of NCI-H1693 cells treated with the selective SMARCA2 degrader PRT3789
The goal of this study was to characterize genome-wide chromatin accessibility changes induced by SMARCA2 degradation in a SMARCA4-deficient non-small cell lung cancer model. NCI-H1693 cells were treated with the selective SMARCA2 degrader PRT3789 (50 nM) or vehicle control (DMSO) for 48 h. ATAC-seq was performed to identify regions of differential accessibility that may help explain the mechanism of synthetic lethality in SMARCA4-deficient contexts. Overall design: NCI-H1693 cells were treated with PRT3789 (50 nM) or DMSO control for 48 h in triplicate.Viable cells were cryopreserved, frozen, and shipped to GENEWIZ (now Azenta Life Sciences) for ATAC-seq library preparation and sequencing . Libraries were sequenced on an Illumina platform to generate paired-end 150 bp reads. Downstream analysis, including quality control, read alignment to the human reference genome (GRCh38), peak calling, and quantification of accessibility, was performed using Pluto Bio (https://pluto.bio). Briefly, paired-end FASTQ files were processed using the nf-core/atacseq pipeline (v2.0). Adapter sequences were removed with Trim Galore. Reads were aligned with Bowtie2 to GRCh38 (NCBI, p.14, release 110) and duplicates were marked and removed from all samples with picard. Peaks were called with macs2 (peak mode: narrow) using a p-value threshold of 0.00001 and an effective genome size of 2,940,000,000. Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER. Peak counts were generated using featureCounts.