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Whole transcriptome analysis with sequencing: methods, challenges and potential solutions

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Abstract

Whole transcriptome analysis plays an essential role in deciphering genome structure and function, identifying genetic networks underlying cellular, physiological, biochemical and biological systems and establishing molecular biomarkers that respond to diseases, pathogens and environmental challenges. Here, we review transcriptome analysis methods and technologies that have been used to conduct whole transcriptome shotgun sequencing or whole transcriptome tag/target sequencing analyses. We focus on how adaptors/linkers are added to both 5′ and 3′ ends of mRNA molecules for cloning or PCR amplification before sequencing. Challenges and potential solutions are also discussed. In brief, next generation sequencing platforms have accelerated releases of the large amounts of gene expression data. It is now time for the genome research community to assemble whole transcriptomes of all species and collect signature targets for each gene/transcript, and thus use known genes/transcripts to determine known transcriptomes directly in the near future.

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Acknowledgments

This work was supported by the Eunice Kennedy Shriver National Institute of Child Health & Human Development of the National Institutes of Health under Award Number R21HD076845 to ZJ. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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The authors have declared that no competing interest exists.

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Authors and Affiliations

  1. Department of Animal Sciences, Washington State University, Pullman, WA, 99164-6351, USA

    Zhihua Jiang, Xiang Zhou, Rui Li, Jennifer J. Michal, Shuwen Zhang & Michael V. Dodson

  2. Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA

    Zhiwu Zhang

  3. Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94720-3200, USA

    Richard M. Harland

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  1. Zhihua Jiang
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Correspondence to Zhihua Jiang.

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Jiang, Z., Zhou, X., Li, R. et al. Whole transcriptome analysis with sequencing: methods, challenges and potential solutions. Cell. Mol. Life Sci. 72, 3425–3439 (2015). https://doi.org/10.1007/s00018-015-1934-y

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