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Innovative Uses of RNAscope

Read about reseachers who take innovative approaches with RNAscope® protocols to advance their research. If you would like to try one of these customer-demonstrated applications, please note that they are non-standard applications and therefore, a careful read through of the publications/materials is highly recommended. Our technical support team is here and will make best efforts to support you.

Customer demonstrated application:
WISH Whole-Mount in situ Hybridization

Our ACD team are excited that Theresa Gross-Thebing, Azadeh Paksa and Erez Raz at Münster University, Germany have driven the RNAscope® technology into a new arena - establishing, optimizing and applying RNAscope® Assay to whole mount embryonic zebrafish samples. Although RNAscope® assay may be applied to any gene and any species, appropriate sample preparation is essential.

Contact the ACD support team at for detailed support for the of RNAscope® Assay.

Theresa Gross-Thebing and Azadeh Paksa have generously volunteered to answer questions specific to the preparation of whole-mount embryonic samples.  Email them using but please note, the response time may take up to 1 week.

A Tips & Tricks and FAQ section surrounding WISH is under development, please check back with us for updates.

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  1. RNAscope® positive control probe:  use zebrafish-specific housekeeping gene for positive control. The Erez Raz Lab used zebrafish myoD gene in channel 2,  CAT # 402461-C2  Dr-myod1-C2.  Alternatively, we also offer CAT# 427301-C2 Dr-gsc-C2 and CAT# 428601 Dr-odc1 (channel 1)
  2. RNAscope® negative control probe: CAT # 310043 Negative Control Probe-DapB
  3. RNAscope® Target Probes:   ACD currently offers 33 zebrafish-specific probes (  New or custom target probes can be designed and manufactured within 2 weeks. 
  4. RNAscope® Assay Reagent Kit:  The Erez Raz Lab used CAT # 320850 RNAscope® Multiplex Fluorescent Reagent Kit, comprise of  three separate components that are also available separately: 
  • CAT # 310091 Wash Buffers
  • CAT # 320842 RNAscope® Pretreatment Kit 
  • CAT # 320851 RNAscope® Multiplex Fluorescent Detection Kit

A multispectral microscopy imaging system is required for visualization. You will be able to investigate up to 4 genes simultaneously with this assay.   Additionally, ACD offers three chromogenic assays; however those assays have not been applied to whole-mount zebrafish embryonic samples.

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