AbstractThe high‐throughput DNA sequencing Illumina Solexa GAII platform was employed to characterize the transcriptome of an antibody‐producing Chinese hamster ovary (CHO) cell line. More than 55 million sequencing reads were generated and mapped to an existing set of CHO unigenes derived from expressed sequence tags (ESTs), as well as several public sequence databases. A very significant fraction of sequencing reads has not been previously seen. The frequency with which fragments of a unigene were sequenced was taken as an estimate of the abundance level of the corresponding transcripts. A wide dynamic range of transcript abundance levels was observed, spanning six orders of magnitude. However, the distribution of coverage across transcript lengths was found to vary, from relatively uniform to highly variable. This observation suggests that more challenges are yet to be resolved before direct sequencing can be used as a true quantitative measure of transcript level and for differential gene expression analysis. With the depth that high‐throughput sequencing methods can reach, one can expect that the entire transcriptome of this industrially important organism will be decoded in the near future. Biotechnol. Bioeng. 2010;105: 1002–1009. © 2009 Wiley Periodicals, Inc.