Zebrafish CRISPR Knock-in Services

Zebrafish CRISPR Knock-in Services


Zebrafish is gaining popularity as a model organism for human genetic disease research. Knock-ins in zebrafish consist of inserting a specific sequence of DNA at a specific site in the zebrafish genome.  The two most popular gene-editing methods used are CRISPR/Cas9 and Tol2.

Point mutation knock-in using CRISPR/Cas9 enables researchers to create zebrafish genetic models in order to understand gene function, basic biology, and more precisely model human diseases.

Our scientists can help you design your next disease model to your precise specifications using CRISPR techniques. Our expertise can help you:

  • Improve your success rate in generating lines
  • Avoid repeating mistakes and reduce variabilities

Our Expertise In Numbers


combined years of CRISPR experience 


genes modified


mutations created


sgRNAs sites tested

Knock-in Techniques

Knock-in is a powerful tool to test the function of specific domains in a protein or to model known human mutations in research animals. These small precise changes in specific amino acid sequence can be used to better understand how gene mutations are associated with human health and disease.

We can successfully repair a point mutation by knocking in a wild-type repair template to restore gene function.  Below is a visual readout of knock-in repair in F0 (injected, generation zero) zebrafish larvae carrying a point mutation in a gene essential for pigmentation. To determine if this repair has been transmitted through the germline, we would subsequently raise these F0 animals to adulthood and screen their progeny for wild-type development of pigment cells. Images were taken at 48 hours post-fertilization (hpf).

Knock-in techniques in zebrafish utilize CRISPR/Cas9 to insert small sequence changes at a specific site in the zebrafish genome. sgRNA site(s) are selected to open the genome adjacent to the desired edit, and a repair template is used to introduce precise changes in the genome. Animals are then raised to adulthood and screened for transmission of the desired edit.

  • Knocking in point mutations. Specific coding sequences can be changed to precisely match genetic variants seen in human disease.
  • Knocking in a fluorescent tag at the native locus. Observe when and where your gene of interest is expressed using fluorescence. A genetically encoded fluorescent marker (GFP, mCherry, etc.) can be inserted in-frame for tagging of either the N- or C-terminus of your protein.
  • Knocking in a protein tag. Genetically encoded tags (FLAG tag, HA-tag, poly(His) tag, etc.) can be inserted in-frame for tagging of either the N- or C-terminus of your protein. The protein can then be observed by Western blots, immunofluorescence, and immunoprecipitation using commercially available common antibodies.
  • Knocking in LoxP sites. Insertion of two LoxP sites flanking your gene of interest creates the ability to eliminate the gene of interest with expression of the Cre recombinase. Cre recombinase can be expressed using tissue or stage-specific promoters for precise control of gene function. Learn more>>

(Left): SelN-BFPSTOP with BFP followed by a STOP codon inserted into the N-terminus of Selenon (SelN). (Center and Right): Ryr1a-mCherry line where the endogenous Ryr1a was tagged with mCherry at the N-terminus. Image courtesy of Melissa A. Wright, MD/PhD, Assistant Professor of Pediatric Neurology at University of Colorado. Read the customer story. 

Modeling STXBP1 Patient Variants in Zebrafish

Illustration of a successful precise point mutation of stxbp 1a in zebrafish. stxbp1a is a highly conserved zebrafish ortholog of human STXBP1 (87% identity). Using CRISPR/Cas9 technology, we were able to precisely generate a benign patient mutation at the conserved amino acid residue (CCC>CTG, p.P94L).

Keys to a Successful Knock-in in Zebrafish

  1. Know your gene - Good knowledge of your gene, alternate isoforms expressed and related orthologs is required for designing an efficient experimental strategy.
  2. Choose good sgRNAs - To ensure you use an sgRNA that guides efficient cutting, 2-3 sgRNAs with different recognition and PAM sites should be designed for each knock-in experiment 
  3. Validate sgRNAs - All sgRNAs should be validated in vivo to ensure that they are not toxic and that they efficiently guide Cas9 cutting of the DNA.
    Read our article on why validation is important.
  4. Create the right donor DNA template - The size of your knock-in insert determines the type of template (double-stranded vs. single-stranded) and the size of the homology arms used.
  5. Design and test primers - Developing a robust assay to detect your edit is critical when you begin screening the embryos produced by the F0 founders.
  6. Screen, Screen, Screen - Knock-ins are notoriously low efficiency, and on top of that, the F0 germline is mosaic and can transmit multiple edits. The rate of transmission to your F1 generation will vary depending on when the F0 germline edit was made in development. Ranges from 3% to 50% have been observed. Be sure to grow enough F1 animals that you will be able to find your F1 heterozygotes. 

Download the infographic: 6 Essential steps to a successful zebrafish knock-in project. 

Download the infographic: Using zebrafish for rapid genetic analysis. 

CRISPR Knock-in Service Options

Standard Injection Mix Validated sgRNA Injection Mix Fully Validated Injection Mix Mosaic Clutch* (F0 injected embryos) Full Build** (Sequence verified heterozygous line)
KI Design
Injection Mix Assembly
Locus Evaluation &
Screening Reagents
InVivo sgRNA Testing
InVivo Editing Assessment
Expertly Injected Embryos
Germline Transmission
Screening & Line Propagation
More DetailsMore DetailsMore DetailsMore DetailsMore Details
* This service is only available to clients in the United States.
** Full Build includes screening n=100 adults; standard husbandry charge applies.

Injection Mix and sgRNA Validation Details

Standard Injection Mix

Choose this option if you want us to pick your sgRNA site, have already tested your sgRNA in vivo, or want to make a CRISPR knockout. We send a custom designed injection mix and you develop your own preferred detection/screening protocol.

What’s Included?
  • Consultation with a genetic engineer to develop the genome editing strategy
  • In silico design of all reagents including the sgRNA site and donor homology template
  • Sequence files for the donor homology construct and edited locus
  • 4 vials of 10uL lyophilized sgRNAs duplexed with the Cas9 protein
  • Injection dyes for early visualization of injection success
  • Detailed Instructions on mix reconstitution and injection protocols.

Validated sgRNA Injection Mix

Choose this option if you want us to guarantee your injection mix is designed around a high efficiency sgRNA site using our rigorous in-house testing process. 

What’s Included?
  • Our Standard Injection Mix PLUS:
  • Selection and testing of two sgRNAs for in vivo evaluation of cutting efficiency
  • Donor homology designed around a demonstrated high efficiency sgRNA site
  • In vivo screening for potential polymorphisms in your target locus

Complete Validated Injection Mix

Choose this option if you want a CRISPR knockin with completely validated reagents to use in your lab and to find your gene edited line. This is the best Custom Injection Mix option for the novice zebrafish line builder.

What’s Included?
  • Full in vivo evaluation of somatic editing efficiency.
  • Confirmation of integration capacity of your edit into the zebrafish genome

Mosaic Clutch (F0 injected embryos)

Choose this option if you want a CRISPR knock-in with completely validated reagents to use in your lab and to find your gene edited line. This is a good option for the researcher who wants to outsource part of the workload in the development of a new line.

What’s Included?
  • Our Complete Validated Injection Mix PLUS:
  • Expertly injected embryos for direct submission to you nursery
  • Fully validated PCR primers and protocols for edit detection assay in your own lab.

Full Build (Sequence verified heterozygous line)

Choose this option if you want us to deliver a stable sequence validated CRISPR knock-in line.

What’s Included?
  • Veried Clutch (F0 injected Embryos) Plus:
  • Growth of F0 injected embryos in our nursery
  • Rigous screening of F0 injected adults for germline transmission of your edit
  • Sequence conformation and propagation of F1 heterozygous animals

Injection Mix Service Component Descriptions

Injection Mix

Injection Mix

We create a mix using quality custom reagents from our validated suppliers. The sgRNAs are duplexed with the Cas9 protein.

The mix is created using concentrations of Cas9, sgRNA and donor homology that work well in our genome editing pipeline. The mix is provided as a stable dehydrated reagent.

Four injection mixes are provided that reconstitute to 5ul of mix each.

  • Custom reagents from validated suppliers
  • Four 10uL lyophilized injection mixes with instructions on reconstitution
  • Rhodamine dye for early visualization of injection success
Screening Reagents

Screening Reagents

Integration efficiency in injected zebrafish embryosYou can miss your edit if you don’t have a good assay to detect it.

We will design and test a robust assay to detect your edit, which is critical when you begin germline screening.

We will also provide PCR primers and protocols for an edit detection assay.

  • PCR primers designed and tested to identify the target edit
  • PCR protocol to identify animals that contain your edit
sgRNA Testing

sgRNA Testing

Ensure that you have the quality reagents you need for a successful genome edit. The efficiency of the sgRNA guided cutting can vary widely and is directly tied to the achievement of a successful genome edit.

Algorithms and experience help us choose the best candidate sgRNAs for your project, but the guided cutting efficiency of an sgRNA can be impacted by genome organization, for example, chromatin accessibility. The best way to determine the effectiveness of an sgRNA in a Zebrafish genome is to test it in vivo in the injected embryos.

We test your sgRNAs for their ability to guide Cas9 cutting. Our process also identifies SNPs and polymorphoisms in your locus that may impact homology directed repair. Embryos are injected with two different sgRNA/Cas9 duplexes and we determine the cutting efficiency for each sgRNA. If both sgRNAs fail to guide successful cutting, a third sgRNA is injected and tested.

Additional sgRNA testing can also be added with consultation.

  • Up to 3 sgRNAs tested for CRISPR cutting efficiency in zebrafish embryos
  • Selection against sgRNAs that have toxic effects
  • Identification of an sgRNA that is successful for guiding CRISPR cutting
In Vivo Editing Efficiency Screening

In Vivo Editing Efficiency Screening

Have total peace of mind by having us test your injection mix in our facility.

Our skilled injectionists will inject embryos with your mix and determine the somatic integration efficiency by PCR.

We will confirm the precise edit by sequencing to ensure that your edit is occurring correctly with no erroneous insertions.

  • Test injection of mix into embryos
  • Integration efficiency in injected embryos
  • Sequencing to confirm precise edit
Expertly Injected Embryos

Expertly Injected Embryos

Our team precisely injects the sg(s) targeting the locus or region of interest, Cas9 protein and the donor homology template to generate F0 embryos.

Germline Transmission Screening & Line Propagation

Germline Transmission Screening & Line Propagation

F0 embryos are reared to adulthood and then screened for germline transmission using a combination of screening techniques to identify germline founders. Identified adults are propagated to ensure a sufficient number of animals to ship to your facility.

Key References

A thorough review of current methods around point mutation knock-ins in zebrafish using CRISPR/Cas9, including the detailed description of the screening workflow for identifying the rare precise editing events generated with current knock-in approaches.

Download the publication.

An excellent overview of knock-ins in zebrafish. The article provides one of the most comprehensive side-by-side comparisons of donor template designs and knock-in strategies available for zebrafish at the time. A detailed discussion of the different repair pathways, template designs, and different reagent choices, as well as their limitations and paths forward for improving knock-in editing efficiencies in the future is very informative

Download the publication.

Boel et al. delve into the dizzying realm of ssODN-mediated knock-in repair with a comprehensive assessment of the impacts of different repair templates and design strategies on editing outcomes. Potential mechanisms of repair that lead to complex mutation patterns obtained with ssODN templates, as well as potential avenues for improvement on these methods are also discussed.

Download the publication.


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