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Guidelines
Suggested parameters and sets of instructions outlining best practices and standards for accomplishing specific animal care and use research duties.

This Copy Was Generated On: June 17, 2026

Guidelines for Acceptable Methods of Identification and Genotyping of Mice, Rats, and Zebrafish

Institutional Animal Care & Use Committee

| Approval Date:

May 4, 2026 10:00 am

Information Only ULAM Staff Research Staff

Summary of Changes

This document has undergone the following changes:

Changed title of document: to change from ‘rodents’ to ‘mice and rats’
Significant reorganization and streamlining of the document to minimize extraneous information and clarify the various methods of identification and genotyping.

Who is Impacted

ULAM Staff
Research Personnel

Impact

A general review of the whole document is recommended.

To describe procedures to safely and appropriately identify and genotype animals used in laboratory research at the University of Michigan.

Responsibility

Investigative personnel are responsible for implementing the approved identification and genotyping methods with oversight and assistance from ULAM personnel, as needed.
The Principal Investigator is responsible for ensuring that all methods of animal identification and genetic sampling that requires removal of tissue are explicitly listed and approved by the Institutional Animal Care and Use Committee (IACUC) in the applicable animal use protocol. The Principal Investigator or designee should consult with ULAM veterinarians if needed, especially if methods other than the ones described in these guidelines are utilized.

Glossary Definitions

Genotyping

The process through which an animal’s genetic make-up is determined using a sample taken from the animal.

Identification

The process of uniquely marking an animal so it can be differentiated from other animals within a group.

Procedures

1. Methods of Cage Identification

Cage Cards
1. Cages must have a visible cage card at all times. Cage cards are an acceptable means of identifying individually housed rodents or groups of rodents for studies where individual identification is not necessary. However, if cage cards are misplaced, animals may not be distinguishable.
2. Include the following required information on the cage card:
  1. Principal Investigator
  2. Protocol number
  3. Account number
  4. Laboratory contact information
  5. Pertinent dates (birth, arrival, surgery, etc.)
  6. Strain or stock, and source or animal
3. The required information may be provided by a pre-printed, electronically generated, bar-coded cage card.

2. Methods of Rodent Identification

Temporary Markings
1. A temporary marking may be used for short-term individual identification, and must be repeated or re-applied as often as necessary to maintain visible markings.
2. There are no restrictions on age of animals.
3. Methods of temporary marking include:
  1. Clipping or shaving fur.
  2. Non-toxic dyes or stains may be used as temporary markings. A small area of fur that is deeply stained is the best method.
    1. Note that certain stains wear off quickly and reapplication is necessary.
  3. A non-toxic “permanent” marker may be used to write numbers, bars, or other distinguishable markings on the tail, fur, or ears.
Implanted MicrochipsFollow manufacturer recommendations for proper placement and use.
1. Improper placement may cause microchips to fall out
2. Use the manufacturer’s injector to place microchips subcutaneously at the back of the neck
3. Verify microchip function with a compatible reader before and after implantation.
4. Microchips may be reused if properly cleaned and sterilized per manufacturer guidelines.
Tattoo
1. Tattooing provides a permanent method of identification, using electric or micro-tattoo equipment.
  1. Electric machines can be used to write numbers or symbols on the tail, ear, or footpads. Training ensures proper technique and legibility.
  2. Microtattooing creates quick dots or symbols and is ideal for neonates.
2. Follow manufacturer recommendations for equipment care, cleaning, and use, including appropriate age of animals.
3. Anesthesia is recommended, as it may aid in the ease of this procedure. Describe anesthetics in the appropriate protocol.
  1. Apply a topical local anesthetic (such as EMLA cream which takes 15 minutes to be effective) to the skin prior to the procedure to reduce post-procedural discomfort.
4. Ink may fade, requiring reapplication, especially if initially performed in neonates.
5. Use sharp and sterile needles. Clean needles between.
6. Disinfect tattoo equipment and needles between cages of animals.
  1. Follow manufacturer recommendations for cleaning electric tattoo equipment including the needle.s.
7. See Appendix C for tattooing equipment options.
Ear Tags
1. Place ear tags when animals are approximately 2-4 weeks of age to ensure animal comfort and appropriate structural integrity of the pinna. Older animals receiving ear tags may experience increased discomfort during placement.
2. Ear tags can fall out if not applied properly or if ears are ripped or torn.
3. Metal and plastic tags are available. Metal ear tags have been associated with inflammatory and neoplastic reactions of the surrounding skin.
Ear Notch or Punch
1. 1. Notch/Punch ears after animals reach 2 weeks of age, when the pinnae (ears) are generally adequately sized.
  2. Ear injury may cause ID loss and animal regrouping may cause confusion between similarly marked animals.
  3. Disinfect equipment before use and between cages of animals.
  4. Use a ear notching scheme that limits the number of notches or punches.
  5. If needed, use the excised tissue as a sample for genotyping, to avoid additional invasive procedures.
Toe Amputation (Toe Clipping)
1. Only utilize toe clipping when no other individual identification method is feasible
2. See Procedures section 3.b.iv below

3. Methods of Collecting Genetic Material for Genotyping

Non-Invasive Methods
1. Fecal Sample
  1. Collect fecal samples from the cage bottom, clean cage or other appropriate container, or as they are excreted during handling.
  2. This method allows for repeat sampling.
  3. Specialized processing methods are needed (see References 6 and 14).
2. Hair Bulb
  1. Pluck a tuft of hair from the ventral body using forceps.
  2. Use a fresh pair of forceps for each animal to avoid cross-contamination (wiping hair is ineffective).
  3. This method allows for repeat sampling.
  4. Specialized processing methods are needed (see References 5 and 13).
3. Saliva
  1. Gently pipette a small amount of PBS into the animal’s mouth to wash the oral cavity, collecting the fluid with the pipet tip.
  2. This method allows for repeat sampling.
  3. Specialized processing methods are needed (see Reference 8).
Invasive Methods
1. Blood
  1. Blood can be drawn from any approved site (see Guidelines on Blood Collection).
    1. This procedure is easiest to perform on mice and rats greater than 8 days of age.
    2. Dried blood spots can be used for analysis.
2. Ear Notch or Punch
  1. Ear notching or punching for identification provides tissue for genotyping. See Procedures Section 2.e for information on use for identification.
  2. Disinfect equipment between animals to prevent sample contamination.
3. Tail Biopsy
  1. The tail biopsy procedure involves cutting through bone or cartilage, blood vessels, nervous tissue and skin.
  2. Perform tail biopsy on animals 21 days of age and younger (ideally days 12-16) to avoid discomfort due to ossified tails.
  3. For animals over 21 days, use anesthesia and preemptive analgesia
    1. Sterile gloves and post-operative monitoring records are not required (not a surgical procedure).
    2. Recover the animal individually in a clean cages; return to housing when fully ambulatory.
  4. Use sterile tools and disinfect between animals or use a new disposable blade for each animal.
  5. Remove only what is necessary from the tail. 2 mm is usually sufficient; total removal cannot exceed 5mm over the animal’s lifetime.
  6. Control hemorrhage using compression, styptic pencils, silver nitrate, tissue adhesives, or cautery.
4. Toe Amputation (Toe Clipping)
  1. Toe amputation involves the removal of the toe at the most distal joint, and is used as both a method of identification and tissue collection for genotyping.
  2. Toe clipping requires skill to minimize pain and distress. Training by a skilled individual is essential; ULAM Training Core or veterinary personnel can assist with training as needed.
  3. Perform toe clipping on animals 7 days of age or younger ideally days 5-7. Remove only the most distal segment (phalanx), preferably from the hind paw, and no more than one toe per foot.
  4. If toe clipping is used for identification and genotyping is necessary, the tissue resulting from identification should serve both purposes. Avoid additional methods of tissue collection (e.g., tail biopsy) unless scientifically necessary.

4. Methods of Zebrafish Genotyping

Fin Clip
1. Zebrafish regenerate caudal fin tissue that is removed. Caution must be used to only remove the fin tissue, and not damage the peduncle or hemorrhaging and permanent tissue damage may occur.
2. Anesthesia is recommended. Alternatively, gentle appropriate restraint (e.g. held with wetted sponge or net and secured with thumb and forefinger) may be used.
3. With a sterile scalpel or scissors, cut up to ½ to 2/3 of the caudal fin.
4. Recover the fish in fresh system water if anesthesia is utilized.

Appendix A: Advantages and Disadvantages of Rodent Identification Methods

Type	Advantages	Disadvantages
Cage Cards	Pertinent information is readily available	Card can be lost or misplaced
Dye (Non-toxic, waterproof)	Easy to apply Non-invasive Identifies individual animals	Temporary
Ear Punch / Notch	Easy to perform Pattern can identify individual animals	ID lost if ear is injured or mutilated Punch / notch can become less readable over time Animals can become indistinguishable if mixed between cages
Ear Tags	Easy to apply Permanent Identifies individual animals	Tags can be lost Animal usually must be restrained to read tag
Tattoo	Permanent Identifies individual animals	Anesthesia recommended Animal may need to be restrained to read tattoo Equipment can be expensive Equipment must be disinfected between use Training required to operate the tattoo instrument
Microchip	Easy to apply Permanent Identifies individual animals Not necessary to restrain animal to read	Expensive Microchip may migrate within the body
Toe Clip (requires scientific justification)	Permanent Pattern can identify individual animals	Requires amputation of a body part Requires anesthesia Usually must restrain animal to read

Appendix B: Advantages and Disadvantages of Rodent Genotyping Methods

Type	Advantages	Disadvantages
Ear notching / punching	Can also serve as a method of identification Easy to perform	Repeat samples cannot be taken if this method is also used for identification
Tail biopsy	Can be performed at an early age Provides a high-quality sample for genotyping	Requires anesthesia and analgesia for older animals Limited amounts can be taken Repeat samples are discouraged Need alternate means of identification
Fecal sample	Repeat samples can be taken Easy to perform	Requires specialized processing methods
Blood sample	Repeat samples can be taken	Requires specialized processing methods
Saliva sample	Repeat samples can be taken	Collection procedure can be difficult Requires specialized processing methods
Hair bulb sample	Repeat samples can be taken Easy to perform	Requires specialized processing methods
Toe amputation (requires scientific justification)	Can also serve as a method of identification	Repeat samples cannot be taken if this method is also used for identification Requires amputation of a body part

Appendix C: Tattoo Equipment Options

Electric Tattoo
1. AIMS – www.animalid.com
2. Harvard Apparatus Tattoo Set – http://www.harvardapparatus.com/webapp/wcs/stores/servlet/haisku3_10001_11051_37781_-1_HAI_ProductDetail_n_37346_37354_37355
Microtattoo
1. Aramis – http://www.ketchum.ca/products/lab-animal/aramis-micro-tattoo-kit OR http://www.braintreesci.com/products.asp?dept=111
2. Fine Science Tools – http://www.finescience.com/Special-Pages/Products.aspx?ProductId=196&CategoryId=39&lang=en-US
Lab Stamp – http://www.somarkinnovations.com

References

Bonaparte D, et al. 2013. FELASA guidelines for the refinement of methods for genotyping genetically-modified rodents. Laboratory Animals 47(3) 134-145
Campbell DB, et al. 1997. Rapid genotyping of mutant mice using dried blood spots for polymerase chain reaction (PCR) analysis. Brain Res Protoc. 1(2):117-23.
Castelhano-Carlos MJ, et al. 2010. Identification methods in newborn C57BL/6 mice: a developmental and behavioural evaluation. Laboratory Animals. 1-16
Dahlborn K, et al. 2013. Report of the Federation of European Laboratory Animal Science Associations Working Group on animal identification. Laboratory Animals 47: 2-11
Gagiliene B, et al. 2014. Direct PCR on Hair: A New Animal-Friendly Genotyping Method. Thermo Fisher Scientific, Inc. Available at: https://www.thermofisher.com/content/dam/LifeTech/global/brands/Documents/1114/App_Note_Direct_PCR_on_Hair_2014_June09_final.pdf
Hamann M, et al. 2010. Non-Invasive Genotyping of Transgenic Mice: Comparison of Different Commercial Kits and Required Amounts. ALTEX. 27(3):185-90.
Hankenson FC, et al. 2008. Evaluation of tail biopsy collection in laboratory mice (Mus musculus): vertebral ossification, DNA quantity, and acute behavioral responses. JAALAS 47(6):10-18
Irwin MH, et al. 1996. Identification of transgenic mice by PCR analysis of saliva. Nat Biotechnol. 14(9):1146-8
Jones CP, et al. 2012. Evaluation of Common Anesthetic and Analgesic Techniques for Tail Biopsy in Mice. JAALAS 51(6): 808-814
NIH Guidelines for Toe Clipping of Rodents. Dec 2013. Available at http://oacu.od.nih.gov/ARAC/documents/Toe_Clipping.pdf
Romano A, et al. 2022. A rapid and inexpensive genotyping method using dried blood spots for mutational analysis in a mutant mouse model: an update. Mol Biol Rep. 49(9):9071-9077
Schaefer DC, et al. 2010. Analysis of physiological and behavioural parameters in mice after toe clipping as newborns. Laboratory Animals. 44:7-13
Schmitteckert EM, et al. 1999. DNA detection in hair of transgenic mice–a simple technique minimizing the distress on the animals. Lab Anim. 33(4):385-9
Symonds EL, et al. 2012. A method for non-invasive genotyping of APCmin/+ mice using fecal samples. Biol Proced Online. 14: 1.

SPECIES: Fish, Amphibians, and Reptiles / Mice / Rats

Questions?

Questions or concerns about the content of this document should be directed to the Unit for Laboratory Animal Medicine (ULAM) at (734) 764-0277 or [email protected].