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