Communication to the Editor

Reaching the depth of the Chinese hamster ovary cell transcriptome†

  1. Nitya M. Jacob1,
  2. Anne Kantardjieff1,
  3. Faraaz Noor Khan Yusufi2,
  4. Ernest F. Retzel3,
  5. Bhanu Chandra Mulukutla1,
  6. Song Hui Chuah2,
  7. Miranda Yap2,
  8. Wei-Shou Hu1,*

Article first published online: 30 OCT 2009

DOI: 10.1002/bit.22588

Issue

Biotechnology and Bioengineering

Biotechnology and Bioengineering

Volume 105, Issue 5, pages 1002–1009, 1 April 2010

Additional Information

How to Cite

Jacob, N. M., Kantardjieff, A., Yusufi, F. N. K., Retzel, E. F., Mulukutla, B. C., Chuah, S. H., Yap, M. and Hu, W.-S. (2010), Reaching the depth of the Chinese hamster ovary cell transcriptome. Biotechnol. Bioeng., 105: 1002–1009. doi: 10.1002/bit.22588

Author Information

  1. 1

    Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE, Minneapolis, Minneapolis 55414-01232, telephone: 612-626-7630; fax: 612-626-7246

  2. 2

    Bioprocessing Technology Institute, A*STAR, Centros, Singapore

  3. 3

    National Center for Genome Resources, Santa Fe, NM 87505

*Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE, Minneapolis, Minneapolis 55414-01232, telephone: 612-626-7630; fax: 612-626-7246.

  1. †

    Nitya M. Jacob and Anne Kantardjieff contributed equally to this work.

Publication History

  1. Issue published online: 19 FEB 2010
  2. Article first published online: 30 OCT 2009
  3. Accepted manuscript online: 30 OCT 2009 12:00AM EST
  4. Manuscript Accepted: 14 OCT 2009
  5. Manuscript Revised: 2 SEP 2009
  6. Manuscript Received: 4 MAY 2009

Funded by

  • NIH Biotechnology Training. Grant Number: GM08347

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

Get PDF (2704K)

Keywords:

  • RNA-Seq;
  • Chinese hamster ovary (CHO) cells;
  • gene expression profiling

Abstract

The 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.

Get PDF (2704K)