Chromosomes in Chinese hamster ovary (CHO) cells are labile. We have shown that high-chromosome-number CHO cells have greater potential to become robust producers of recombinant proteins. One explanation being the increase in transgene integration sites. However, high-chromosome-number cell clones produce more IgG3 following culture of single-cell clones, even under conditions that yield the same number of integrations as cells with normal chromosome numbers. Here, we characterized high-chromosome-number cells by transcriptome analysis. RNA standards were used to normalize transcriptomes of cells that had different chromosome numbers. Our results demonstrate that the mRNA ratio of beta-actin and many other genes in high-chromosome-number cells to that in normal-chromosome-number cells per cell (normalized to RNA standards) was smaller than the equivalent genomic size and cell volume ratios. Many genes encoding membrane proteins are more highly expressed in high-chromosome-number cells, probably due to differences in cell size caused by the increase in chromosomes. In addition, genes related to histone modification and lipid metabolism are differentially expressed. The reduced transcript level required per protein produced in total and the different intracellular signal transductions might be key factors for antibody production. (C) 2019, The Society for Biotechnology, Japan. All rights reserved.