Abstract
Gene expression analysis in the tumor microenvironment using archived clinical samples is challenging because of formalin fixation, RNA degradation, and limiting sample volume. NanoString gene expression profiling is a RNA–DNA hybrid capture technology that does not require PCR and can accurately quantify the expression of to 800 transcripts in a single reaction. The technology requires 50–100 ng of RNA, which can be degraded (EDITOR: is this correct?) to a 200 bp fragment size. In contrast to amplification technologies, nanoString counts the actual numbers of transcripts that are captured with transcript-specific and fluorescently-barcoded probes. This chapter describes protocols for RNA extraction, quantification, mRNA and miRNA profiling and data analysis.
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Acknowledgements
The Molecular Pathology Centre at Jewish General Hospital is grateful to the Jewish General Hospital Foundation and all participants of the Enbridge Ride to Conquer Cancer® event who have enabled the purchase of the nCounter Analysis System. The images in Figs. 1 and 2 were reproduced from nanoString publications with the consent from nanoString® Technologies, Inc.
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M’Boutchou, MN., van Kempen, L.C. (2016). Analysis of the Tumor Microenvironment Transcriptome via NanoString mRNA and miRNA Expression Profiling. In: Ursini-Siegel, J., Beauchemin, N. (eds) The Tumor Microenvironment. Methods in Molecular Biology, vol 1458. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3801-8_21
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DOI: https://doi.org/10.1007/978-1-4939-3801-8_21
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Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3799-8
Online ISBN: 978-1-4939-3801-8
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