HCR hairpin
In Situ HCR v3.0

State-of-the-art mRNA imaging:

  • Simple: 2-stage enzyme-free protocol
  • Amplified: Signal elevated above autofluorescence
  • Multiplexed: Simultaneous 1-stage amplification for up to 5 targets
  • Quantitative: Signal scales linearly with target abundance
  • Penetrating: Whole-mount vertebrate embryos and thick tissue sections
  • Resolved: Subcellular or single-molecule resolution as desired
  • Sensitive: Single molecules detected in thick autofluorescent samples
  • Versatile: Suitable for use with diverse targets in diverse organisms
  • Compatible: Combine with tissue clearing as desired
  • Robust: Automatic background suppression throughout the protocol

Multiplexed mRNA imaging in a whole-mount chicken embryo using in situ HCR v3.0
without probe set optimization (Choi et al., 2018).

In situ HCR supports four multiplexed quantitative analysis modes:

  • qHCR imaging: Analog mRNA relative quantitation with subcellular resolution in an anatomical context
  • dHCR imaging: Digital mRNA absolute quantitation via single-molecule imaging in an anatomical context
  • qHCR flow cytometry: Analog mRNA relative quantitation for high-throughput expression profiling of mammalian and bacterial cells
  • qHCR northern blots: Relative and absolute quantitation of RNA target size and abundance

In Situ HCR v2.0 Image Gallery

Multiplexed mRNA imaging in a whole-mount zebrafish embryo using in situ HCR v2.0.
(Choi et al., 2014, movie)
Multiplexed mRNA imaging using in situ HCR v2.0 in diverse organisms.
(zoo paper: Choi et al., 2016, movies: fruit fly, sea urchin, zebrafish, chicken, mouse)