Total RNA was isolated from 15 EACs and Barrett’s metaplasia samples (13 non-dysplastic Barrett’s mucosa, six low-grade dysplasia (LGD), and seven high-grade dysplastic samples) using Trizol (Invitrogen) followed by RNeasy column purification (Qiagen, Germantown, MD), cRNA generation and hybridization to U133A GeneChips (Affymetrix, Santa Clara, CA). Data have been deposited in GEO (GSE37203).8 (link) Hybridizations and array image analysis was performed by the University of Michigan DNA Microarray Core Facility. A filtering algorithm was used to select genes with either increased or decreased expression in adenocarcinomas or dysplastic BE when compared with BE samples. A twofold change in gene expression was considered significant.29 (link) To normalize the microarray data, a summary statistic was calculated using the robust multichip average method30 (link) as implemented in the Affymetrix library of the Bioconductor version 1.3 that provides background adjustment, quantile normalization, and summarization. Expression values for each sample were then compared with the mean expression value for the seven Barrett’s metaplasia samples.