Straightforward Multiplexing

Using HCR v3.0 probe sets and amplifiers for multiplexed RNA fluorescence in situ hybridization (RNA-FISH), RNA flow cytometry, or northern blotting, protocols are simple, robust, and enzyme-free, requiring only 2 stages independent of the number of target RNAs:

Detection Stage

During the detection stage, orthogonal probe sets are hybridized in parallel. 


Amplification Stage

During the amplification stage, orthogonal HCR amplifiers carrying spectrally distinct fluorophores operate in parallel.

Detection Stage

Amplification Stage

​Normal Sleep Schedule

We favor protocols employing an overnight probe incubation step to enable researchers to maintain a normal sleep schedule. Protocol durations can be customized as desired based on sample thickness and assay format. 

Orthogonal HCR Amplifiers

HCR amplifiers are programmable, enabling straightforward multiplexing using orthogonal HCR amplifiers programmed to operate independently. Currently, we offer a catalog of 5 orthogonal HCR amplifiers labeled with any of 5 Alexa Fluor® dyes. HCR amplifiers can also be custom-labeled with any of the other Alexa Fluor® dyes or Cyanine 5.5 or 7. HCR signal amplification is quantitative, 1-step, isothermal, and enzyme-free. Learn more

Custom Probe Set Design

Custom probe set design is available for any target mRNA in any organism across the tree of life. Learn more

 Orthogonal HCR probe sets

Orthogonal HCR amplifiers

Simple 2-stage enzyme-free protocol