HCR RNA-FISH: Protocol Overview
The same 2-stage protocol is used independent of the number of target RNAs.
HCR™ RNA-FISH Products
Multiplexed, quantitative, high-resolution RNA imaging
HCR™ 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™ Flow Cytometry and Northern Blots
The same probe sets and amplifiers enable multiplexed quantitative:
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RNA flow cytometry (how HCR™ RNA flow cytometry works)
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northern blotting (how HCR™ northern blotting works)
with automatic background suppression throughout the protocol.
Simple Robust Protocols
HCR™ RNA-FISH protocols are simple, robust, and enzyme-free, requiring only 2 stages independent of the number of target RNAs.
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.
Straightforward Multiplexing
HCR™ enables straightforward multiplexing using 1-step quantitative signal amplification for all target RNAs simultaneously.
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.
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.
Custom Probe Design
Free custom probe design is available for any target mRNA in any organism across the tree of life.
HCR™ Protein-IF + HCR™ RNA-FISH
Combine HCR™ RNA-FISH bundles with HCR™ protein-IF bundles for simultaneous multiplexed, quantitative, high-resolution protein and RNA imaging with 1-step HCR™ signal amplification for all protein and RNA targets simultaneously.
Quantitative RNA Analysis Modes
HCR™ enables four quantitative analysis modes for RNA targets:
Subcellular Quantitative RNA Imaging
Subcellular RNA imaging provides analog RNA relative quantitation with subcellular resolution in the anatomical context of thick autofluorescent samples.
Single-Molecule Quantitative RNA Imaging
Single-molecule RNA imaging provides digital RNA absolute quantitation with single-molecule resolution in the anatomical context of thick autofluorescent samples.
Quantitative RNA Flow Cytometry
Quantitative RNA flow cytometry provides analog RNA relative quantitation for high-throughput expression profiling of mammalian cells and bacteria.
Quantitative Northern Blots
Quantitative northern blots provide relative and absolute quantification of RNA target size and abundance.
HCR™ Probe Set
Probe sets are designed by the Molecular Instruments Team.
To assist with your research, sequence information for probe binding sites is available for your orders upon request.
HCR™ Amplifier
Metastable fluorescent hairpins are quality-control tested by the Molecular Instruments Team.
HCR™ Buffers
Probe hybridization buffer
Probe wash buffer
Amplification buffer
HCR™ RNA-FISH Bundle
Conveniently order reagents as a bundle containing any of: probe set, amplifier, buffers. Safety Data Sheets
Getting started?
For multiplexed, quantitative, high-resolution HCR™ RNA-FISH with automatic background suppression throughout the protocol:
✓ order one HCR™ probe set per target RNA (each for use with a different HCR™ amplifier)
✓ order one HCR™ amplifier per probe set (each with a different fluorophore)
✓ order HCR™ buffers
The same reagents can be used for multiplexed quantitative HCR™ RNA flow cytometry and northern blots with automatic background suppression throughout the protocol.