RNAscope Technology | Assay selection Guide
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.
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.
Please click the options below to navigate.
> RNAscope ISH Manual Assays
> Leica Automated Assays
> Roche Automated Assays
RNAscope ISH Manual Assays
|
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
|
Leica Automated Assays
In this strategic partnership, ACD has developed an automated RNA ISH workflow for the Leica BOND Rx IHC ISH platform.
|
|
RNAscope 2.5 Leica Assay - BROWN |
RNAscope 2.5 Leica Assay - RED |
RNAscope 2.5 Leica Duplex Assay |
RNAscope Leica Multiplex Fluorescent Assay |
BaseScope Leica Assay - RED |
miRNAscope Leica Assay - RED |
|
Automated System |
Leica BOND RX System |
Leica BOND RX System |
Leica BOND RX System |
Leica BOND RX System |
Leica BOND RX System |
Leica BOND RX System |
|
Assay Type |
Chromogenic |
Chromogenic |
Chromogenic |
Fluorescent |
Chromogenic |
Chromogenic |
|
Dye Used |
Diaminobenzidine (DAB) |
Fast Red |
DAB & Fast Red Option for Green & Fast Red |
TSA-based Vivid / Opal fluorophores |
Fast Red |
Fast Red |
|
Multiplexing |
Singleplex |
Singleplex |
Singleplex, Duplex |
Single to Fourplex |
Singleplex |
Singleplex |
|
Key Benefit |
Robust, sensitive, permanent stain Most widely used RNAscope assay |
Provides bright color stains with high contrast to background |
Simultaneous in situ detection of two RNA species |
Utilizes up to 4 different spectral channels providing high flexibility |
Specific detection of splice variants/exon junctions and short targets |
Robust and specific detection of small RNAs |
|
Ideal for |
High throughput Routine applications |
Studies of tissues with endogenous color background such as melanin in skin, liver, or lung from smokers |
Co-localization studies to map co-expression of two targets (e.g., secreted ligand and its receptor) |
Co-localization studies of up to 4 gene simultaneously Experimental application requiring flexibility |
Detection of splice variants and exon junctions, short insertions/deletions, short targets of complex & highly homologous gene families |
Detection of small RNAs including ASOs, miRNAs, piRNAs, shRNAs, siRNAs, and tRNAs |
|
Novel Gene or Unknown Expression |
Compatible |
Compatible |
Compatible |
Compatible |
Compatible |
Compatible |
|
Archival Specimens |
Compatible |
Compatible |
Compatible |
Compatible |
Compatible |
Compatible |
|
Microscope Imaging System |
Standard bright field |
Standard bright field |
Standard bright field |
Multispectral fluorescent imaging |
Standard bright field |
Standard bright field |
|
Sample Type |
FFPE |
FFPE |
FFPE |
FFPE Tissues (TMAs) |
FFPE |
FFPE |
|
Quantitation Method |
Visual inspection |
Visual inspection |
Visual inspection |
Visual inspection |
Visual inspection |
Visual inspection |
|
# of tissue sections per kit |
60 (20 mm x 20 mm) |
60 (20 mm x 20 mm) |
60 (20 mm x 20 mm) |
60 (20 mm x 20 mm) |
60 (20 mm x 20 mm) |
60 (20 mm x 20 mm) |
|
Target Sequence length required |
300-1000bp |
300-1000bp |
300-1000bp |
300-1000bp |
50-300bp |
17-50bp |
Roche Automated Assays
ACD has developed an automated RNA ISH workflow solution for use with the Roche Ventana and Benchmark ISH & IHC Staining Platforms.
|
|
RNAscope VS Universal HRP Assay |
RNAscope VS Universal AP Assay |
RNAscope VS Duplex Assay |
BaseScope VS Assay - RED |
|
Automated System |
Roche DISCOVERY ULTRA |
Roche DISCOVERY ULTRA |
Roche DISCOVERY ULTRA |
Roche DISCOVERY ULTRA |
|
Detection Options |
Chromogenic/ Fluorescent |
Chromogenic |
Chromogenic |
Chromogenic |
|
Chromogen Used |
•Diaminobenzidine (DAB)
•Purple
•Teal
•Green
•FAM
•FITC
•Red610
•Rhodamine
•Rhodamine 6G
•Cy5
•DCC
|
Fast Red |
•DAB & Fast Red
•Teal & Fast Red
•Green & Fast Red
|
Fast Red |
|
Reaction/Staining Type |
Singleplex |
Singleplex |
Singleplex, Duplex |
Singleplex |
|
Key Benefit |
Robust, sensitive, permanent stain Most widely used RNAscope assay. |
Robust, sensitive, permanent stain. |
Simultaneous in situ detection of two RNA targets |
Specific detection of splice variants/exon junctions and short targets |
|
Ideal for |
High throughput Routine applications |
High throughput Routine applications |
Co-localization studies to map co-expression of two targets (e.g., secreted ligand and its receptor) |
Detection of splice variants and exon junctions, short insertions/deletions, short targets of complex & highly homologous gene families |
|
Novel Gene or Unknown Expression |
Compatible |
Compatible |
Compatible |
Compatible |
|
Archival Specimens |
Compatible |
Compatible |
Compatible |
Compatible |
|
Microscope Imaging |
Standard bright field/ Fluorescent |
Standard bright field |
Standard bright field |
Standard bright field |
|
Sample Type |
FFPE |
FFPE |
FFPE |
FFPE |
|
Quantitation Method |
•Visual inspection
•HALO® SOFTWARE
•Any open-source image analysis software
|
•Visual inspection
•HALO® SOFTWARE
•Any open-source image analysis software
|
•Visual inspection
•HALO® SOFTWARE
•Any open-source image analysis software
|
•Visual inspection
•HALO® SOFTWARE
•Any open-source image analysis software
|
|
#Oftissue sections per kit |
60 (20 mm x 20 mm) |
60 (20 mm x 20 mm) |
60 (20 mm x 20 mm) |
60 (20 mm x 20 mm) |
|
Target Sequence length required. |
300-1000bp |
300-1000bp |
300-1000bp |
50-300bp |
CiteAb Awards
CiteAb 2024 Award Winner
This kit enables high-plex spatial co-detection of RNA and protein markers for the Standard BioTools Hyperion™ Imaging Mass Cytometry (IMC) System. This technology caught our judges' eye as a really powerful research tool to help advance discovery.
CiteAb 2024 Highly Commended
"The Highly Commended Honor given to our ACD brand underscores our Spatial Biology team's dedication to enriching our customers' experiences and prioritizing researchers' needs."
- Kim Kelderman President & CEO of Bio-Techne