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-IHC + HCR RNA-FISH
Combine HCR RNA-FISH bundles with HCR protein-IHC 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:
qHCR RNA Imaging
qHCR RNA imaging provides analog RNA relative quantitation with subcellular resolution in the anatomical context of thick autofluorescent samples.
dHCR RNA Imaging
dHCR RNA imaging provides digital RNA absolute quantitation with single-molecule resolution in the anatomical context of thick autofluorescent samples.
qHCR RNA Flow Cytometry
qHCR RNA flow cytometry provides analog RNA relative quantitation for high-throughput expression profiling of mammalian cells and bacteria.
qHCR Northern Blots
qHCR northern blots provide relative and absolute quantification of RNA target size and abundance.
HCR Probe Set
HCR split-initiator 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 HCR 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.