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RNAscope ISH Technology Manual Assays

Techniques for detection of RNA in situ (ISH and FISH) have been around for years, as have the perceived gold standards of microarrays and PCR.  However, these techniques lack clinically relevant information regarding spatial expression in the cellular and tissue microenvironment. 

Our scientists at Advanced Cell Diagnostics, revolutionized the RNA ISH method and in 2011 introduced RNAscope ISH for spatial detection of target RNA within intact single cells. With its proprietary probe design, to simultaneously amplify target-specific signals and suppress background noise from non-specific hybridization, RNAscope ISH is now a proven technology that is available in both manual and automated formats. 


The most widely used RNAscope Assay.

Available in both chromogenic and fluorescent labels.

May be used as single plex, duplex, fourplex, and HiPlex formats.

Robust, sensitive, and archivable results.


Used to detect small non-coding RNAs including miRNAs, ASOs, and siRNAs.

Visualize gene regulation with spatial and morphological context.

Detection via single plex and chromogenic Fast Red.


Detects exon junctions, splice variants, short/highly homologous RNA sequences, and point mutations.

Sensitive detection at single-nucleotide differences.

Available in single (red) or Duplex kits.


Detects and qualifies gene copy number (amplifications/detections) and gene rearrangements/fusions.

Hi-res and precise target detection for small genomic regions/single gene focus.

A chromogenic Duplex assay (red/blue) visualized using brightfield microscopy.

RNA-Protein Co-Detection Assay

Enables simultaneous detection of cell-type specific gene expression and secreted proteins.

Correlate RNA-Protein expression and visualize cell margin and RNA targets.

Acquire more data and conserve precious samples.


Based on ACD’s patented signal amplification and background suppression technology, the RNAscope Assay uses a novel and proprietary method of chromogenic in situ hybridization (ISH) to visualize and spatially detect single RNA molecules at the single cell level, whilst maintaining the spatial tissue microenvironment. Recognized as the most sensitive RNA ISH method, it may be used for low expressing gene targets. Independent of your genes of interest, our RNAscope ISH Assay uses common reagents and protocols, providing universal conditions. For simultaneous detection of multiple genes in nearly any tissue type, using fluorescent labels, the RNAscope Multiplex Fluorescent Assays are ideal.


The miRNAscope Assay allows for the visualization of ASO, miRNA, siRNA, and other nucleic acid targets between 17-50 nucleotides expression with single-cell resolution, preserving spatial and morphological context. Detection of small non-coding RNAs such as microRNAs and short oligonucleotide therapeutics such as ASO and siRNA require a robust, highly specific, and sensitive assay with minimal time and effort, and while microarrays and PCR both provide useful molecular profiles of diseases, important clinically relevant cell and tissue context information is lost along with the spatial variation of gene expression patterns.


The unique BaseScope Assay enables the visualization of a specific RNA locus at single cell sensitivity with spatial and morphological context. Used in applications such as the detection of exon junctions/splice variants, short/highly homologous RNA sequences (50-300 bases) and point mutations, the BaseScope assay can detect these in the single cell, in situ using a single Z pair, with down to a single (one) nucleotide difference.


The new chromogenic DNA in situ hybridization (ISH) technology, DNAscope Duplex Assay enables accurate and reliable detection of DNA aberrations and spatial arrangements of DNA, where current commercially available fluorescent in situ hybridization (FISH) techniques fall short, lacking single gene detection specificity and limiting the scale and development of DNA research.

DNAscope ISH employs the proven “double-Z” probe design and signal amplification system of RNAscope, enabling rapid and flexible probe development for any DNA target or spatial arrangement and can be easily visualized in paraffin embedded tissues, via standard brightfield microscopy.

ICW Co-Detection

The recently added Integrated Co-Detection Workflow (ICW) Assays, or RNA-Protein Co-Detection Assays allow researchers to simultaneously examine cell-type specific gene expression and identify cellular sources of secreted proteins. As with other RNAscope ISH technology assays, you can detect your targets of interest, spatially within the tissue microenvironment and enable inclusion of a wider range of antibodies to be combined with RNA ISH, thereby allowing researchers to acquire more data and conserve precious samples.