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Gene Expression Profiling Using 3′ Tag Digital Approach

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Expression Profiling in Neuroscience

Part of the book series: Neuromethods ((NM,volume 64))

Abstract

Massive parallel sequencing will become the method of choice for transcriptome profiling. Two protocols have been developed to quantify level of expressions: full-length RNA sequencing (RNA-SEQ) and 3′ tag digital gene expression (DGE). We have studied the performance of 3′ tag DGE profiling and used this protocol to compare the expression profiles of brain RNA to universal human reference RNA. This comparison highlighted that DGE is highly quantitative with excellent correlation of differential expression with quantitative real-time PCR. Our analysis also showed that when compared to microarray, one lane of 3′ DGE sequencing had wider dynamic range for transcriptome profiling and was able to detect expressed genes that are below the detection threshold of microarray. We conclude that 3′ tag DGE profiling is highly sensitive and reproducible for transcriptome profiling. It outperforms microarray platforms in detecting lower abundant transcripts.

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Acknowledgments

This work was supported by Donna Foundation for breast cancer research, NIH Grants AI 33144, AI 48793, AI 40065, and 1 UL1 RR024150-01 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health, and the NIH Roadmap for Medical Research.

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Authors and Affiliations

  1. Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic Comprehensive Cancer Center, Rochester, MN, USA

    Yan W. Asmann & Jean-Pierre A. Kocher

  2. Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Rochester, MN, USA

    E. Aubrey Thompson

Authors
  1. Yan W. Asmann
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  2. E. Aubrey Thompson
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  3. Jean-Pierre A. Kocher
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Correspondence to Jean-Pierre A. Kocher .

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Editors and Affiliations

  1. , Laboratorie de Physiopathologie de la Ba, Université d'Artois, rue Jean Souvraz 9, Lens, 62307, France

    Yannis Karamanos

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Asmann, Y.W., Thompson, E.A., Kocher, JP.A. (2012). Gene Expression Profiling Using 3′ Tag Digital Approach. In: Karamanos, Y. (eds) Expression Profiling in Neuroscience. Neuromethods, vol 64. Humana Press. https://doi.org/10.1007/978-1-61779-448-3_5

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  • DOI: https://doi.org/10.1007/978-1-61779-448-3_5

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-447-6

  • Online ISBN: 978-1-61779-448-3

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