Skip to main content

Why use RNAscope ISH?

Standard molecular methods for disease profiling rely on dissociated cells that results in a loss of spatial information. However, a more complete and contextual understanding of the molecular mechanisms underlying cellular behavior requires complementary information on the subcellular localization of events, something that is only possible by use of in situ hybridization. The RNAscope assay, a novel multiplex nucleic acid ISH technology with a patented probe design, amplifies target-specific signals but not background noise, delivering clear and actionable results with high sensitivity and specificity.

Key RNAscope ISH Technology Applications

Advanced Cell Diagnostics, leaders in the emerging field of spatial genomics and spatial transcriptomics, offers a unique RNAscope in situ hybridization assay, that enables visualization of gene expression at a single cell level, within an intact tissue.  

 RNAscope ISH Technology can be applied over many applications, learn more about key areas of focus, including neuroscience, cancer, immune-oncology, cell and gene therapy and single-cell analysis.  

Getting Started with RNAscope ISH Technology

Similar to solving a jigsaw puzzle, successfully performing the technique of in situ hybridization (ISH) benefits from a systematic, stepwise approach that concentrates on one stage of the process at a time, then moves onto the next. ACD’s RNAscope ISH Technology represents a huge advance in the power and ease of use of ISH, greatly simplifying and streamlining time-tested methods while routinely delivering single-molecule detection levels of sensitivity. While not as simple as doing a four-piece jigsaw puzzle, we have made ISH considerably easier than it was formerly.

RNAscope ISH Technology Manual Assays 

Techniques for detection of RNA in situ (ISH and ISH) 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. 

RNAscope

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.

miRNAscope

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.

BaseScope

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.

DNAscope

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.

RNA ISH Technology Automated Assays

The RNAscope in situ Hybridization Technology has been developed for both manual and automated protocols.  If you require high throughput or an automated solution, ACD has partnered with Leica Biosystems and Roche Tissue Diagnostics, to deliver RNAscope ISH automated assays. 

Leica Biosystems Inc.

In this strategic partnership, we have developed an automated RNA ISH workflow for the Leica BOND Rx IHC ISH platform

Roche Tissue Diagnostics

We have developed an automated RNA ISH workflow solution for use with the Roche Ventana and Benchmark ISH & IHC Staining Platforms.

RNAscope ISH Technology Assay Selection Table

  RNAscope HD BROWN or RED RNAscope Duplex RNAscope Multiplex Fluorescent (V2) RNAscope HiPlex BaseScope BaseScope Duplex miRNAscope DNAscope
Assay Type Chromogenic Chromogenic Fluorescent Fluorescent Chromogenic Chromogenic Chromogenic Chromogenic
Plexing offered Singleplex Duplex 4-Plex 12-Plex; up to 48-Plex SinglePlex Duplex SinglePlex Duplex
Dye used DAB - HRP or Fast Red - ALP Green - HRP Fast Red - ALP TSA Plus/Opal dyes Alexa 488, Atto 550, Atto 647N, Alexa 750 Fast Red - ALP Green - HRP Fast Red - ALP Fast Red - ALP Fast Red - ALP
Channel Channel 1 Channel 1, 2 Channel 1, 2, 3, 4 Tail 1, 2, … 12 Channel 1 Channel 1, 2 Channel S1 Channel 1, 2
Available Platform
  • Manual
  • Ventana
  • Discovery Ultra
  • Leica Bond Rx 
  • Manual
  • Ventana
  • Discovery Ultra
  • Leica Bond Rx 
  • Manual
  • Leica Bond Rx
  • Manual
  • Manual
  • Ventana
  • Discovery Ultra
  • Leica Bond Rx 
  • Manual
  • Manual
  • Leica Bond Rx
  • Manual
Target Size >300 nt >300 nt >300 nt >300 nt 50-300 nt 50-300 nt 17-50 nt

>3000 nt (Vector/Viral) and

>20,000 nt (Chromosomal)​ nucleotides

Sample Type
  • FFPE
  • Fixed Frozen
  • Fresh Frozen
  • Cultured Cells
  • Whole Mount*
  • FFPE
  • Fixed Frozen
  • Fresh Frozen
  • Cultured Cells
  • Whole Mount*
  • FFPE
  • Fixed Frozen
  • Fresh Frozen
  • Cultured Cells
  • Whole Mount*
  • Fixed Frozen
  • Fresh Frozen
  • Cultured Cells
  • Whole Mount*
  • FFPE
  • Fixed Frozen
  • Fresh Frozen
  • Cultured Cells
  • Whole Mount*
  • FFPE
  • Fixed Frozen
  • Fresh Frozen
  • Cultured Cells
  • Whole Mount*
  • FFPE
  • Fixed Frozen
  • Fresh Frozen
  • Cultured Cells
  • FFPE
Professional Assay Services PAS

Professional Assay Services

Professional Assay Services provides GCLP-compliant RNAscope, BaseScope, miRNAscope, and DNAscope in situ hybridization (ISH) assay services to support clinical and pre-clinical studies for our academic and biopharma partners.

Download the Professional Assay Service Brochure

Related RNAscope Resources

Single-Cell Application Note

The RNAscope multiplex in situ hybridization technology enables the incorporation of spatial mapping and confirmation of gene signatures into single cell RNA sequencing workflows

RNAscope-GeoMx DSP White Paper

Molecularly Guided Highly Multiplexed Spatial Profiling with the RNAscope and GeoMx Assays

Dual ISH-IHC App note

Combining the RNAscope ISH technology with IHC to spatially resolve RNA and protein targets simultaneously