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Profiling conserved microRNA expression in recombinant CHO cell lines using illumina sequencing

Authors

  • Stephanie Hammond,

    1. Department of Chemical Engineering, University of Delaware, Newark, Delaware
    2. Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, Delaware 19711; telephone: +1-302-831-0344; fax: +1-302-831-4841
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  • Jeffrey C. Swanberg,

    1. Department of Chemical Engineering, University of Delaware, Newark, Delaware
    2. Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, Delaware 19711; telephone: +1-302-831-0344; fax: +1-302-831-4841
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  • Shawn W. Polson,

    1. Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, Delaware 19711; telephone: +1-302-831-0344; fax: +1-302-831-4841
    2. Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware
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  • Kelvin H. Lee

    Corresponding author
    1. Department of Chemical Engineering, University of Delaware, Newark, Delaware
    2. Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, Delaware 19711; telephone: +1-302-831-0344; fax: +1-302-831-4841
    • Department of Chemical Engineering, University of Delaware, Newark, Delaware.
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Abstract

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate multiple aspects of cell physiology. The differential expression of conserved miRNAs in two Chinese hamster ovary (CHO) cell lines producing recombinant proteins was examined relative to the CHO-K1 cell line. A total of 190 conserved CHO miRNAs were identified through homology with known human and rodent miRNAs. More than 80% of these miRNAs showed differential expression in recombinant CHO cell lines. The small RNA sequencing data were analyzed in context of the CHO-K1 genome to examine miRNA organization and develop sequence-specific miRNA resources for CHO cells. The identification and characterization of CHO miRNAs will facilitate the use of miRNA tools in cell line engineering efforts to improve product yield and quality. Biotechnol. Bioeng. 2012; 109:1371–1375. © 2011 Wiley Periodicals, Inc.

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