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HCR™ RNA Flow Cytometry Protocols

Multiplexed quantitative RNA flow cytometry

HCR™ RNA flow probe sets, amplifiers, and buffers enable multiplexed quantitative high-throughput expression profiling of mammalian cells and bacteria with automatic background suppression throughout the protocol (how HCR™ RNA flow cytometry works). 

HCR™ RNA Flow Cytometry: Protocol Overview

Detection Stage

Amplification Stage


The same 2-stage protocol is used independent of the number of target RNAs.


Simple Robust Protocols

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

Automatic Background Suppression

HCR™ RNA flow 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.

Custom Probe Design

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

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.


Quantitative Single-Cell Signal

HCR™ RNA flow cytometry enables single-cell relative RNA quantitation for mammalian cells and bacteria.


Download HCR™ RNA Flow Protocols

HCR™ RNA Flow Cytometry Protocols

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