TY - JOUR
T1 - Analysis of the Tumor Microenvironment Transcriptome via NanoString mRNA and miRNA Expression Profiling
AU - M'Boutchou, Marie-Noël
AU - van Kempen, Léon C
PY - 2016
Y1 - 2016
N2 - 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.
AB - 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.
KW - Gene Expression Profiling/methods
KW - Humans
KW - MicroRNAs/genetics
KW - Neoplasms/genetics
KW - Quality Control
KW - RNA, Messenger/genetics
KW - Transcriptome
KW - Tumor Microenvironment/genetics
U2 - 10.1007/978-1-4939-3801-8_21
DO - 10.1007/978-1-4939-3801-8_21
M3 - Article
C2 - 27581030
SN - 1064-3745
VL - 1458
SP - 291
EP - 310
JO - Methods in Molecular Biology
JF - Methods in Molecular Biology
ER -