HCR RNA-FISH: Protocol Overview
The same 2-stage protocol is used independent of the number of target RNAs.
Custom Probe Design
HCR probe sets comprising one or more split-initiator probe pairs enable multiplexed quantitative RNA fluorescence in situ hybridization (RNA-FISH), RNA flow cytometry, and northern blotting with automatic background suppression throughout the protocol.
If your target is not already in our catalog, the Molecular Instruments Team offers free custom probe design for any target mRNA in any organism across the tree of life (view gallery).
Please provide the accession number (if available) or the target RNA sequence (including 5' and 3' UTRs) when you place your order.
Simple Robust Protocols
Protocols for HCR RNA-FISH, HCR RNA flow cytometry, and HCR northern blotting 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.
Image Any mRNA. In Any Organism. In Any Sample Type.
HCR RNA-FISH 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.
HCR Protein-IHC + HCR RNA-FISH
Combine HCR IHC probes with HCR RNA-FISH probes to enable HCR protein-IHC + HCR RNA-FISH for multiplexed quantitative protein and RNA imaging with 1-step HCR signal amplification for all protein and RNA targets simultaneously.
Quantitative RNA Analysis Modes
HCR split-initiator probe sets enables four quantitative analysis modes for RNA targets:
qHCR RNA Imaging
qHCR RNA imaging enables analog RNA relative quantitation with subcellular resolution in the anatomical context of thick autofluorescent samples.
dHCR RNA Imaging
dHCR RNA imaging enables digital RNA absolute quantitation with single-molecule resolution in the anatomical context of thick autofluorescent samples.
qHCR Flow Cytometry
qHCR RNA flow cytometry enables analog RNA relative quantitation for high-throughput expression profiling of mammalian cells and bacteria.
qHCR Northern Blots
qHCR RNA northern blots enable simultaneous quantification of RNA target size and abundance.
A new era for in situ hybridization:
multiplexed, quantitative, high-resolution, sensitive, versatile, robust
RNA relative quantitation for high-throughput expression profiling of mammalian cells and bacteria
Custom Probe Design
✓ Image any mRNA in any organism in any sample type
✓ Straightforward multiplexing
✓ Quantitative amplified signal
✓ Automatic background suppression throughout the protocol
✓ Rapid worldwide delivery
✓ Volume discounts
✓ No design fees