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HCR™ IF + HCR™ RNA-FISH Protocols

Simultaneous multiplexed, quantitative, high-resolution protein and RNA imaging 

HCR™ IF probes, amplifiers, and buffers and HCR™ RNA-FISH probe sets, amplifiers, and buffers enable a unified approach to multiplexed quantitative high-resolution immunofluorescence (IF) and RNA fluorescence in situ hybridization (RNA FISH; how HCR™ IF + HCR™ RNA-FISH works)

HCR™ IF + HCR™ RNA-FISH: Protocol Overview

Protein Detection Stage

RNA Detection Stage

Amplification Stage


The same 3-stage protocol is used independent of the number of protein and RNA targets.


Quantitative 1-step enzyme-free HCR™ signal amplification for all protein and RNA targets simultaneously


Simple Robust Protocols

HCR™ IF + HCR™ RNA-FISH protocols are simple, robust, and enzyme-free, requiring only 3 stages independent of the number of protein and RNA targets.

Straightforward Multiplexing

HCR™ enables straightforward multiplexing using 1-step quantitative signal amplification for all protein and RNA targets simultaneously.

Any organism across the tree of life

Free custom probe design for any target mRNA in any organism. For protein targets, plug-and-play using your own 1º antibodies of choice (without modification) in combination with validated HCR™ 2º antibody probes.

Normal Sleep Schedule

We favor protocols with an overnight probe incubation step to enable researchers to maintain a normal sleep schedule; durations can be customized as desired based on sample thickness.


Simultaneous Quantitative High-Resolution Protein and RNA Imaging

Subcellular protein and RNA imaging enables protein and RNA relative quantitation with subcellular resolution in the anatomical context of highly autofluorescent samples.

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