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

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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.

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Acknowledgments

This study was supported by the Chinese State Key Projects for Basic Research (2004CB518707) and Beijing Municipal Key Project (D0905001040731). We would like to thank Dr. Ting Xiao for her helpful discussion and support, Bangrong Cao for his help with the analysis, and Bing Ling for his advice on biological experiments.

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Authors and Affiliations

  1. State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100021, People’s Republic of China

    Lin Feng, Yu Liu, Suping Guo, Hongwei Zheng, Yanning Gao, Shujun Cheng & Kaitai Zhang

  2. BGI Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, 518083, People’s Republic of China

    Hang Liu, Zhike Lu, Guangwu Guo, Jian Wang & Yong Zhang

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  1. Lin Feng
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  2. Hang Liu
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  3. Yu Liu
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  4. Zhike Lu
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  5. Guangwu Guo
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  6. Suping Guo
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  7. Hongwei Zheng
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  8. Yanning Gao
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  9. Shujun Cheng
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  10. Jian Wang
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  11. Kaitai Zhang
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  12. Yong Zhang
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Corresponding authors

Correspondence to Kaitai Zhang or Yong Zhang.

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Feng, L., Liu, H., Liu, Y. et al. Power of Deep Sequencing and Agilent Microarray for Gene Expression Profiling Study. Mol Biotechnol 45, 101–110 (2010). https://doi.org/10.1007/s12033-010-9249-6

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