title: Analysis of the Tumor Microenvironment Transcriptome via NanoString mRNA and miRNA Expression Profiling.
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 (
  
  
  
  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.
authors: Lady Davis Institute for Medical Research, McGill University, Montréal, QC, Canada.
authors: Marie-Noël
authors: MN
authors: M'Boutchou
authors: Lady Davis Institute for Medical Research, McGill University, Montréal, QC, Canada. leon.vankempen@mcgill.ca.|Department of Pathology, Molecular Pathology Center, Jewish General Hospital, 3755 Cote Sainte Catherine Road, Room E618, Montréal, QC, Canada, H3T 1E2. leon.vankempen@mcgill.ca.
authors: Léon C
authors: LC
authors: van Kempen
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology*; D011786:Quality Control; D012333:RNA, Messenger / Q000235:genetics*; D059467:Transcriptome; D059016:Tumor Microenvironment / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger
keywords: NanoString; mRNA and miRNA expression profiling