Zebrafish swabbing

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The text on this page is taken from an informal compilation of opinions of contributors to the online VOLE List. As such, they are not peer reviewed and may contain differences of opinion. Those wishing to contact the list may contact Adrian Smith.

Is anyone using skin swabbing for genotyping in zebrafish, and if so would you be prepared to share your protocol? We'd like to introduce it at one of our units but are getting some push back from one of the researchers. It would be really helpful to know if anyone out there is already doing it successfully.

Zebrafish swabbing protocol below:-

1.     Adult fish to be swabbed are individually removed from the tank and held securely in an aquarium net on top of a wet sponge.

2.     Using the tip of the Snooplex FastPrep swab, the fish are stroked gently from the operculum to the caudal fin while rotating the swab around its axis, five times.

3.     The fish are immediately placed into a marked tank and returned to the aquatic system on designated rack for individual tanks.

4.     The Snooplex FastPrep swab will be placed into a 1.5 ml reaction tube and DNA extraction performed in accordance with the standard protocols. Analyse the tissue (typically 1-2 days).

5.     Once analysis is complete, house them in groups dependent on whether they tested positive for the gene modification. Note on the tank label the determined genotype, and ensure it is labelled correctly with the appropriate stock number, strain and date of birth.

Comparison with fin clipping below:-

Snooplex gDNA extraction gDNA extraction from Fin-clipping
Time Less time consuming

(time saved approx.66%)

More time consuming    
Analgesia Not required Required (HPRA authorisation)
Anaesthesia Not required Required (HPRA authorisation)
Quantity Good conc. (ng/μl) Good conc. (ng/μl)          
Quality Good gel PCR products, RFLP digests and sequencing traces     Good gel PCR products, RFLP digests and sequencing traces
Ethics Ethical Exemption required

(University Animal Research Ethics Committee)

Project Authorisation Required

(National Health Products Regulatory Agency)

Commercial kits Works best with proprietary reagents Works well with commercially available reagents
Cost Approx. €3-4/sample Approx. €1-2/sample      
Genotyping assays Compatible with all tested methods of genotyping Compatible with all methods of genotyping        
Skill level Requires Training Requires Training and Individual Authorisation
Animal Size Not suitable on younger fish <3 months old Amenable to animals from juvenile stage onwards