Advanced Cell Diagnostics

RNAscope® and BaseScope™ Assays Overview

The RNAscope® and BaseScope™ Assays are based on the proprietary RNAscope® Technology, enabling RNA target expression analysis within intact cells and tissues with high sensitivity and specificity.


RNAscope® Assay
The innovative RNAscope® Assay, with in situ hybridization technology to detect mRNA and ncRNA targets of >300bp, was launched in 2011 and marks the foundation of our product portfolio.  The proprietary probe design requires an average of 20 Z pairs per target, however a minimum hybridization of 6 Z pairs can be used to obtain a signal. With over 800 publications in peer-reviewed journals, across multiple disciplines, the RNAscope® Assay represents a revolutionary advance in in situ target RNA detection.


BaseScope™ Assay
The BaseScope™ Assay is a recent addition to the RNAscope® Technology product portfolio, launched in early 2016.  Using the same innovative technology and proprietary probe design as used in the RNAscope Assay, the BaseScope™ Assay is further refined to detect as few as 1-3 Z pairs. This powerful in situ hybridization technology enables the specific detection of exon junctions, short target/splice variants highly homologous sequences and point mutations, with single cell detection sensitivity in a broad range of tissues, samples and species.

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RNAscope® and BaseScope™ Assay Comparison

 RNAscope® AssayBaseScope™ Assay
Number of ZZ Pair per target Standard probe design is 20 ZZ probes (minimum of 6 ZZ probes) 1 to 3 ZZ probes based on the application
Target mRNA >300 bases
lncRNA > 300 bases
Exon junctions/Splice Variants
RNA 50 to 300 bases
Validated point mutations
Application lcnRNA and mRNA >300 bases Exon junctions/splice variants, circular RNA, gene fusion, gene knockout
Short/highly homologous sequences, TCRs and CDR sequence for T cell clones, pre-miRNA, gene editing/CRISPR, CAR-T cell validation and detection
Point mutation, short InDel, homologues
Multiplex capability Single to up to 12-plex Single to Duplex
Detection Chromogenic or fluorescent Chromogenic
Sample type FFPE cells & tissues (TMAs)
Fresh frozen tissues
Fixed frozen tissues
Cultured cells
FFPE cells & tissues (TMAs)
Fresh frozen tissues
Fixed frozen tissues
Cultured cells
Pretreatment kit Reagent Kit includes Universal Pretreatment Kit Reagent kit includes Universal Pretreatment Kit
Kit RNAscope® kit* BaseScope™ kit*
Probe RNAscope® probe* BaseScope™ probe*
Automation Available on Leica Bond Rx and Ventana Discovery ULTRA Singleplex available on Leica Bond Rx and Ventana Discovery ULTRA

*RNAscope® and BaseScope™ Assay products components cannot be interchanged.

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