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RNAscope™, BaseScope™ and miRNAscope™Assays

The RNAscope™, BaseScope™, and miRNAscope™ 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.

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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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miRNAscope™ Assay

The miRNAscope Assay uses an advanced innovative in situ hybridization technology and proprietary probe design to enable highly specific and sensitive detection of small RNAs including antisense oligonucleotides (ASOs), microRNAs (miRNAs), and small interfering RNAS (siRNAs), with single cell resolution providing spatial and morphological context. 

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RNAscope, BaseScope, and miRNAscope Assay Comparison



 RNAscope AssayBaseScope AssaymiRNAscope Assay
Number of ZZ Pair per targetStandard probe design is 20 ZZ probes (minimum of 6 ZZ probes)1 to 3 ZZ probes based on the applicationN/A
TargetmRNA >300 bases
lncRNA > 300 bases
Exon junctions/Splice Variants
RNA 50 to 300 bases
Validated point mutations
Small RNAs 17-50 bases
ASOs, miRNAs, siRNAs
ApplicationlcnRNA and mRNA >300 basesExon 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
Small RNAs 17-50 bases
ASOs, miRNAs, piRNAs, shRNAs, siRNAs, and tRNAs
Multiplex capabilitySingle to up to 12-plexSingle to DuplexSingle-plex
DetectionChromogenic or fluorescentChromogenicChromogenic
Sample typeFFPE cells & tissues (TMAs)
Fresh frozen tissues
Fixed frozen tissues
Cultured cells
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 kitReagent Kit includes Universal Pretreatment KitReagent kit includes Universal Pretreatment KitReagent kit includes Universal Pretreatment Kit
KitRNAscope kit*BaseScope kit*miRNAscope kit*
ProbeRNAscope probe*BaseScope probe*miRNAscope probe*
AutomationAvailable on Leica Bond Rx and Ventana Discovery ULTRASingleplex available on Leica Bond Rx and Ventana Discovery ULTRAAvailable on Leica Bond Rx

*RNAscope, BaseScope, and miRNAscope Assay products components cannot be interchanged.

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Advanced Cell Diagnostics

Our new headquarters office starting May 2016:

7707 Gateway Blvd.  
Newark, CA 94560
Toll Free: 1 (877) 576-3636
Phone: (510) 576-8800
Fax: (510) 576-8798



19 Barton Lane  
Abingdon Science Park
OX14 3NB
United Kingdom
Phone 2: +44 1235 529449
Fax: +44 1235 533420



Advanced Cell Diagnostics China

Building 15, No. 26 Xihuan South Road
Beijing Economic-Technological Development Area
Beijing, China, Zip code: 100176

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