Molecular Biotechnology

, Volume 45, Issue 2, pp 101–110

Power of Deep Sequencing and Agilent Microarray for Gene Expression Profiling Study

  • Lin Feng
  • Hang Liu
  • Yu Liu
  • Zhike Lu
  • Guangwu Guo
  • Suping Guo
  • Hongwei Zheng
  • Yanning Gao
  • Shujun Cheng
  • Jian Wang
  • Kaitai Zhang
  • Yong Zhang
Research

DOI: 10.1007/s12033-010-9249-6

Cite this article as:
Feng, L., Liu, H., Liu, Y. et al. Mol Biotechnol (2010) 45: 101. doi:10.1007/s12033-010-9249-6

Abstract

Next-generation sequencing-based Digital Gene Expression tag profiling (DGE) has been used to study the changes in gene expression profiling. To compare the quality of the data generated by microarray and DGE, we examined the gene expression profiles of an in vitro cell model with these platforms. In this study, 17,362 and 15,938 genes were detected by microarray and DGE, respectively, with 13,221 overlapping genes. The correlation coefficients between the technical replicates were >0.99 and the detection variance was <9% for both platforms. The dynamic range of microarray was fixed with four orders of magnitude, whereas that of DGE was extendable. The consistency of the two platforms was high, especially for those abundant genes. It was more difficult for the microarray to distinguish the expression variation of less abundant genes. Although microarrays might be eventually replaced by DGE or transcriptome sequencing (RNA-seq) in the near future, microarrays are still stable, practical, and feasible, which may be useful for most biological researchers.

Keywords

Gene expression profilingDigital Gene Expression tag profiling (DGE)MicroarrayReal-time PCRDifferentially expressed genes

Supplementary material

12033_2010_9249_MOESM1_ESM.xls (7.5 mb)
(XLS 7685 kb)

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Lin Feng
    • 1
  • Hang Liu
    • 2
  • Yu Liu
    • 1
  • Zhike Lu
    • 2
  • Guangwu Guo
    • 2
  • Suping Guo
    • 1
  • Hongwei Zheng
    • 1
  • Yanning Gao
    • 1
  • Shujun Cheng
    • 1
  • Jian Wang
    • 2
  • Kaitai Zhang
    • 1
  • Yong Zhang
    • 2
  1. 1.State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingPeople’s Republic of China
  2. 2.BGI Shenzhen, Bei Shan Industrial ZoneShenzhenPeople’s Republic of China