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

M'Boutchou, M-N. & van Kempen, L. C., 2016, In : Methods in Molecular Biology. 1458, p. 291-310 20 p.

Research output: Contribution to journalArticleAcademicpeer-review

UNLABELLED: 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.

Original languageEnglish
Pages (from-to)291-310
Number of pages20
JournalMethods in Molecular Biology
Publication statusPublished - 2016


  • Gene Expression Profiling/methods, Humans, MicroRNAs/genetics, Neoplasms/genetics, Quality Control, RNA, Messenger/genetics, Transcriptome, Tumor Microenvironment/genetics

ID: 76698778