In Vitro Technologies :: RNAscope and BaseScope Assays

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.

RNAscope® and BaseScope™ Assay Comparison

comp rna scope

Resources

> More Information on RNAscope

> More Information on Base Scope

	RNAscope^® Assay	BaseScope™ 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.