Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples.

ABSTRACT: Next-generation sequencing requires accuracy, reproducibility, and standardized reference materials. The Sequencing Quality Control (SEQC-2) multicenter studies on paired breast cancer and B cell lines generated extensive genomic datasets, but integrated epigenomic and proteomic references remain limited. Here, we performed Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Methyl-seq, RNA sequencing (RNA-seq), and proteomic profiling to establish comprehensive multi-omics reference materials. We identified >7,700 protein groups, with 95% of genes encoding a single peptide isoform. Protein expression from CpG island (CGI)-overlapping transcripts was higher than non-CGI transcripts in both cell lines. Certain SNVs were incorporated into mutated peptides. Chromatin acces

SUBMITTER: Nepal C 

PROVIDER: S-EPMC12853167 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature