HCR RNA-FISH: Protocol Overview
The same 2-stage protocol is used independent of the number of target RNAs.
All major
automation platforms
HCR™ RNA-FISH Protocols
Multiplexed, quantitative, high-resolution RNA imaging
HCR™ RNA-FISH probe sets, amplifiers, and buffers enable multiplexed, quantitative, high-resolution RNA fluorescence in situ hybridization (RNA-FISH) with automatic background suppression throughout the protocol (how HCR™ RNA-FISH works).
HCR™ RNA-FISH: 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-FISH protocols are simple, robust, and enzyme-free, requiring only 2 stages independent of the number of target RNAs.
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Automatic Background Suppression
HCR™ RNA-FISH 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.
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Straightforward Multiplexing
HCR™ enables straightforward multiplexing using 1-step quantitative signal amplification for all target RNAs simultaneously.
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Deep Sample Penetration
HCR™ amplification hairpins are short predominantly double-stranded oligos that penetrate thick samples to execute an enzyme-free amplification cascade at the site of the target.
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Image Any Target mRNA. In Any Organism. In Any Sample Type.
HCR™ offers unmatched versatility (see gallery): FFPE tissue sections, fresh/fixed frozen tissue sections, thick brain slices, cells in solution or on a slide, whole-mounts, cleared samples, model organisms, non-model organisms, environmental samples, or multi-kingdom samples.
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Custom Probe Design
Free custom probe design is available for any target mRNA in any organism across the tree of life.
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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.
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HCR™ IF + HCR™ RNA-FISH
HCR™ IF + HCR™ RNA-ISH protocols enable multiplexed, quantitative, high-resolution protein and RNA imaging with 1-step HCR™ signal amplification for all protein and RNA targets simultaneously.
Quantitative High-Resolution RNA Imaging
HCR™ RNA-FISH enables quantification of RNA targets with subcellular and single-molecule resolution in an anatomical context using two complementary imaging modes (see subcellular/single-molecule comparison):
Subcellular Quantitative RNA Imaging
Subcellular RNA imaging enables analog RNA relative quantitation with subcellular resolution in the anatomical context of thick autofluorescent samples.
Single-Molecule Quantitative RNA Imaging
Single-molecule RNA imaging enables digital RNA absolute quantitation with single-molecule resolution in the anatomical context of thick autofluorescent samples.
