HCR v3.0

A new era for in situ hybridization

✓  Simple

✓  Amplified

✓  Multiplexed

✓  Quantitative

✓  Penetrating 

✓  Resolved

✓  Sensitive

✓  Portable

✓  Versatile

✓  Compatible

✓  Robust

2-stage enzyme-free protocol 

Signal elevated above autofluorescence 

Simultaneous 1-step amplification for up to 5 target RNAs

Signal scales linearly with target abundance

Whole-mount vertebrate embryos and thick tissue sections

Subcellular or single-molecule resolution as desired

Single molecules detected in thick autofluorescent samples

Suitable for use with diverse targets in diverse organisms

Multiple assay formats: RNA-FISH, RNA flow cytometry, northern blots

Combine with tissue clearing as desired  

Automatic background suppression throughout the protocol

Multiplexed, quantitative, sensitive, versatile, robust

Thick Autofluorescent Samples

Third-generation in situ hybridization chain reaction (HCR) redefines the state-of-the-art for RNA fluorescence in situ hybridization (RNA-FISH) in thick autofluorescent samples including whole-mount vertebrate embryos.

Straightforward Multiplexing 

Orthogonal HCR amplifiers enable 1-step signal amplification for up to 5 target RNAs simultaneously. Learn more

Automatic Background Suppression

HCR v3.0 reagents provide automatic background suppression throughout the protocol, ensuring that even if probes or amplifiers bind non-specifically in the sample they will not generate amplified background, dramatically enhancing performance and ease-of-use. Learn more 

Deep Sample Penetration 

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

Two Quantitative Imaging Modes

qHCR Imaging

Analog RNA relative quantitation with subcellular resolution in an anatomical context. Learn more 

dHCR Imaging

Digital RNA absolute quantitation with single-molecule resolution in an anatomical context. Learn more 

Simple Robust Protocols

HCR v3.0 protocols are simple, robust, and enzyme-free, requiring only 2 stages independent of the number of target RNAs. Learn more

Any Organism Across the Tree of Life

No matter what your sample (whole-mount embryo, thick brain slice, FFPE tissue section, model or non-model organism, mammalian cells, bacterial cells, multi-species environmental sample), we are happy to help! View Gallery

HCR v3.0
Probe sets, amplifiers, buffers
RNA fluorescence in situ hybridization (RNA-FISH)
✓ Multiplexed, quantitative, sensitive, versatile, robust

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