top of page

HCR™ RNA Flow Cytometry Technology

Multiplexed quantitative RNA flow cytometry

HCR™ probe sets, amplifiers, and buffers enable multiplexed quantitative RNA flow cytometry with automatic background suppression throughout the protocol, enabling high-throughput RNA expression profiling of mammalian cells and bacteria without the need to engineer reporter lines.


Quantitative Signal

HCR™ signal is quantitative in the form of single-cell fluorescence intensities that scale approximately linearly with the number of RNA target molecules per cell. 

HCR™ RNA Flow Cytometry: How It Works

Detection Stage


Amplification Stage


Detection Stage

An HCR™ probe set comprises multiple probe pairs that hybridize to different subsequences along the target. Initiator i1 is split between each pair of probes such that only probe pairs that hybridize specifically to the target RNA colocalize the full initiator i1.

Amplification Stage

An HCR™ amplifier comprises metastable fluorescent hairpins h1 and h2. Specifically bound probe pairs that colocalize full initiator i1 trigger growth of a tethered fluorescent amplification polymer. 

Automatic Background Suppression

HCR™ probes and amplifiers combine to provide automatic background suppression throughout the protocol: probes that bind non-specifically do not colocalize full initiator i1 and do not trigger amplification; hairpins that bind non-specifically are kinetically trapped and do not trigger amplification.

Quantitative RNA Flow Cytometry in Mammalian Cells and Bacteria


Redundant 2-Channel Detection

To illustrate the quantitative nature of HCR™ RNA flow cytometry, we detect a target mRNA using two probe sets that trigger different amplifiers carrying spectrally distinct fluorophores.  

Mammalian Cells (HEK 293T)

Bacteria (E. coli)


High Accuracy and Precision

The resulting scatter plots of single-cell signal demonstrate high accuracy (linearity with zero intercept) and precision (tight scatter around the line) in mammalian cells and bacteria.


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 cytometry 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.

Precision Increases with Probe Set Size

Quantitative precision increases with probe set size due to the benefits of automatic background suppression. For quantitative HCR™ flow cytometry, we recommend using 30+ split-initiator probe pairs per target RNA (maximize probe set size given target length). 

Signal-to-Background Increases with Amplification Time 

For quantitative HCR™ flow cytometry, we recommend overnight amplification to grow long amplification polymers that enhance the signal-to-background ratio. 


Reagents will not generate amplified background even if they bind non-specifically within the sample


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


Custom probe set design for any target mRNA in any organism across the tree of life

Quantitative HCR™ RNA Flow Cytometry

 RNA relative quantitation

✓ High accuracy and precision

✓ High-throughput single-cell analysis

✓ Mammalian cells or bacteria

✓ Automatic background suppression throughout the protocol

bottom of page