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Analysis of the Tumor Microenvironment Transcriptome via NanoString mRNA and miRNA Expression Profiling

  • Marie-Noël M’Boutchou
  • Léon C. van Kempen
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1458)

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.

Key words

NanoString mRNA and miRNA expression profiling 

Notes

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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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Marie-Noël M’Boutchou
    • 1
  • Léon C. van Kempen
    • 1
    • 2
  1. 1.Lady Davis Institute for Medical ResearchMcGill UniversityMontréalCanada
  2. 2.Department of Pathology, Molecular Pathology CenterJewish General HospitalMontréalCanada

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