Epigenomic Profiling of Primary Gastric Adenocarcinoma Reveals Super-enhancer Heterogeneity [SNP]

Regulatory elements in cancer remain poorly characterized in primary solid tumors. Here we applied microscale histone modification profiling to delineate the landscape of somatic promoters and super-enhancers in primary gastric adenocarcinoma, analyzing 94 epigenomic profiles of primary tumors, normal tissues, and cell lines Genomic DNA extracted from gastric tumors and matched gastric non-malignant (normal) tissues was hybridized on Affymetrix SNP6 genotyping arrays. Normal samples (n=98) from this accession and 25 samples from GSE31168 were used to construct reference models by Affymetrix Genotyping Console 4.2. Five samples from GSE36138 were also reanalyzed in this study. Please note that a collective of normal SNP6 profiles were used to construct a reference model, which was used to normalise the cancer profiles. The copy number changes in the cancer profiles were then detected. The descriptions field contains details about each normal SNP6 profile that used for building the reference model for specified cancer profiles and corresponding processed file name. The 'readme_re-analysis.txt' contains the details about the re-analyzed samples (e.g. sample characteristics, sample-to-file association etc.).