Gene Therapy/AAV

Adeno-associated virus (AAV) has proven to be an effective gene therapy delivery vehicle. The primary considerations in gene therapy preclinical in vivo animal studies are vector biodistribution, cell-specific uptake and transgene expression, as well as safety against germ line transmission.  While assays of extracted RNA and DNA from bulk tissue are simple, these provide only an average value for an entire complex tissue and lack cellular resolution.


RNA and DNA in situ hybridization using RNAscope™ and BaseScope™ assays combine the quantitative, molecular measurement, like PCR, with single-cell resolution in the context of intact tissue morphology.  Moreover, RNAscope enables simultaneous detection of AAV vector DNA and transgene mRNA expression, and it can be multiplexed with cell markers.  It is a simple and reliable method for analysis of AAV in routine FFPE tissues.


  • AAV vector DNA detection and quantification in intact fixed tissue
  • Probes designed to AAV promoter regions and anti-sense strand from AAV DNA detection
  • Detection of therapeutic human- and codon-optimized transgene RNA without cross-hybridization to endogenous transcripts
  • Morphology-based AAV vector biodistribution and transgene mRNA expression analysis in intact animal model tissues
  • Visual and quantifiable assays to measure percentage of cells positive for vector and transgene expression
  • Multiplexed analysis of cell-specific AAV and transgene mRNA with cell marker probes, e.g., neuronal, astrocyte, glia, hepatocytes, Kupfer cell markers

Fig 1. Identification of specific cells transduced by AAV-GFP following subretinal injection using the RNAscope 2.5 HD Duplex assay to simultaneously detect the CB promoter DNA sequence of the AAV vector (green) and the GFP transgene mRNA (red). Staining was observed in almost all of the retinal layers (with the exception of the choroid) in the transduced region, but no staining was observed in the non-transduced naïve region.



BaseScope staining allows visualization and quantification of transgene expression (red arrow) and AAV vector (green arrow) presence in treated liver samples

Fig 2. BaseScope staining allows visualization and quantification of transgene expression (red arrow) and AAV vector (green arrow) presence in treated liver samples



Catalog Probes (Ex: CMV, CBA, WPRE, etc.)

Search Catalog Control & Target Probes

If your gene of interest in not listed in our catalog, ACD can design and manufacture new in situ hybridization probes for you, To order or get more info on Made-to-Order New Targets Probes, please fill in the form below and an ACD Account Executive will contact you.

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Professional Assay Services

  • Unparalleled expertise in RNAscope and BaseScope ISH
  • High capacity and high throughput, delivering more than 10,000 slides per year
  • Supporting dozens of gene therapy companies for research studies enabling pre-IND submission
  • Team of specialists perform quantitative image analysis using HALO™ Software (Indica Labs)
  • Board-certified pathologist review
  • Actionable results delivered in weeks rather than months
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Recorded Webinar

Visual detection and quantification of AAV and LV vector biodistribution and transgene expression in preclinical animal models with RNAscope and BaseScope™ in situ hybridization.

Application Note

Application note "Detection of immune cell checkpoint and functional markers in the tumor microenvironment by the RNA in situ hybridization RNAscope assay'



Flyer "Tissue-Based Gene Therapy Biodistribution Analysis Using RNAscope in situ Hybridization"

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