Chinese hamster ovary (CHO) cells are the most widely used host for large scale production of recombinant therapeutic proteins exhibiting high productivities in the gram per liter range. Although these cells have been extensively characterized and optimized, a demand to further increase the performance towards higher productivity and clonal stability exists. Up to date, the clone selection process is mainly based on phenotypic screens like titer measurements and growth data instead of more reliable biomarkers. Recently, the genomes of Chinese hamster as well as of different CHO cell lines were sequenced, assembled and annotated [1–3]. This new information gives the opportunity for functional analysis of the transcriptome and allows rational designs for the identification of biomarkers for clone selection and targets for cell line engineering.