Integrated multiomics profiling of isogenic STAG1 and STAG2 knockout cancer cell lines across multiple tumour contexts

We generated isogenic STAG1 and STAG2 knockout cancer cell lines across multiple tumour types to systematically assess paralogue-specific impacts on chromatin and gene regulation. Experimental design included matched wild-type controls and independent knockout clones per context. We applied an integrated multiomics workflow: in situ Hi-C to profile 3D genome architecture (compartment/TAD/loop analyses), ATAC-seq to quantify chromatin accessibility and regulatory element activity, RNA-seq (poly(A) or rRNA-depletion as appropriate) to measure transcriptome changes, and quantitative mass spectrometry–based proteomics to assess protein abundance. Standardized pipelines were used for data processing and quality control, including read alignment to the human reference genome, replicate concordance assessment, library complexity metrics, and normalization. Differential and integrative analyses evaluated paralogue-specific and context-dependent effects across assays, with cross-modality linkage between chromatin topology, accessibility, transcription, and proteome profiles. The study provides harmonized, assay-specific datasets with accompanying metadata enabling reuse and comparative analysis of STAG1 versus STAG2 perturbations in cancer cell models.