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HCR™ RNA-FISH Products

Multiplexed, quantitative, high-resolution RNA imaging

HCR™ probe sets, amplifiers, and buffers enable multiplexed, quantitative, high-resolution RNA fluorescence in situ hybridization (RNA-FISH) with automatic background suppression throughout the protocol (how HCR™ RNA-FISH works).


HCR™ Flow Cytometry and Northern Blots

The same probe sets and amplifiers enable multiplexed quantitative:

with automatic background suppression throughout the protocol.


Simple Robust Protocols

HCR™ RNA-FISH protocols are simple, robust, and enzyme-free, requiring only 2 stages independent of the number of target RNAs.

Automatic Background Suppression

HCR™ RNA-FISH reagents provide automatic background suppression throughout the protocol, ensuring that even if probes or hairpins bind non-specifically in the sample they will not generate amplified background, dramatically enhancing performance and ease-of-use.

Straightforward Multiplexing

HCR™ enables straightforward multiplexing using 1-step quantitative signal amplification for all target RNAs simultaneously.

Deep Sample Penetration

HCR™ amplification hairpins are short predominantly double-stranded oligos that penetrate thick samples to execute an enzyme-free amplification cascade at the site of the target.

Image Any Target mRNA. In Any Organism. In Any Sample Type. 

HCR™ offers unmatched versatility (see gallery): FFPE tissue sections, fresh/fixed frozen tissue sections, thick brain slices, cells in solution or on a slide, whole-mounts, cleared samples, model organisms, non-model organisms, environmental samples, or multi-kingdom samples. 


Custom Probe Design

Free custom probe design is available for any target mRNA in any organism across the tree of life. 


Combine HCR™ RNA-FISH bundles with HCR™ protein-IF bundles for simultaneous multiplexed, quantitative, high-resolution protein and RNA imaging with 1-step HCR™ signal amplification for all protein and RNA targets simultaneously. 


Quantitative RNA Analysis Modes

HCR™ enables four quantitative analysis modes for RNA targets: 

Subcellular Quantitative RNA Imaging

Subcellular RNA imaging provides analog RNA relative quantitation with subcellular resolution in the anatomical context of thick autofluorescent samples.


Single-Molecule Quantitative RNA Imaging

Single-molecule RNA imaging provides digital RNA absolute quantitation with single-molecule resolution in the anatomical context of thick autofluorescent samples.

Quantitative RNA Flow Cytometry

Quantitative RNA flow cytometry provides analog RNA relative quantitation for high-throughput expression profiling of mammalian cells and bacteria.


Quantitative Northern Blots

Quantitative northern blots provide relative and absolute quantification of RNA target size and abundance.

HCR™ Probe Set


Probe sets are designed by the Molecular Instruments Team.

To assist with your research, sequence information for probe binding sites is available for your orders upon request.

HCR™ Amplifier


Metastable fluorescent hairpins are quality-control tested by the Molecular Instruments Team. 

HCR™ Buffers


Probe hybridization buffer

Probe wash buffer

Amplification buffer



Conveniently order reagents as a bundle containing any of: probe set, amplifier, buffers. Safety Data Sheets

Getting started?

For multiplexed, quantitative, high-resolution HCR™ RNA-FISH with automatic background suppression throughout the protocol:


 order one HCR™ probe set per target RNA (each for use with a different HCR™ amplifier)

 ✓ order one HCR™ amplifier per probe set (each with a different fluorophore)

 ✓ order HCR™ buffers

The same reagents can be used for multiplexed quantitative HCR™ RNA flow cytometry and northern blots with automatic background suppression throughout the protocol. 

All major 

automation platforms 

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