Mouse Search 101: Tips for Searching the JAX® Mice Repository
The Jackson Laboratory currently distributes more than 9,000 mouse strains, and we typically bring in 500 or more new strains every year. Searching our ever-expanding catalog for mouse models of interest is not always straightforward. Here, I will familiarize you with the JAX® Mice database’s search functionalities and share with you strategies to help you to search for mice as efficiently as possible.
In the beginning, there was the JAX® Mice Search page...
It all starts with our JAX® Mice Search page. Unlike the search box on the top of JAX.org webpages, which searches all pages on the JAX website, the search field here ONLY searches for JAX® Mice. Using the tabs at the top of the search box, you can search either by stock number (Stock #) or by keyword. Each tab turns dark blue when activated.
If you happen to already know the Stock # of the strain you are looking for:
- Click on the “Search by Stock #” tab.
- Enter the Stock #.
- Click on “Go” to the right of the search box (or “Enter” on your keyboard).
This will take you directly to the strain datasheet.
For searches by gene names or symbols, transgenes, strain names, disease models, or phenotypes, use the “Keyword Search” tab. (This is the default search tab when the page loads.) Simply start typing your preferred keyword. The search box has integrated auto-filling and refinement capabilities to make such searches easier and more efficient, so you likely will be presented with several auto-fill options. As a general rule, most searches will be more effective if you take advantage of our search engine’s auto-filling capabilities.
Making a choice in the auto-fill dropdown will immediately run the search. If no options appear, don’t despair (at least, not yet!). Just hit “Enter” on your keyboard after entering your search term. Results matching your search term will come up with the results. If you have trouble finding a strain of interest, try removing descriptors like “knockout,” “KO,” “null,” “floxed,” etc. You will see how to use those terms for refining searches later.
Let’s try an example: let’s say you are looking for OT1 mice (a transgenic mouse that expresses a T cell receptor (TCR) that recognizes an ovalbumin peptide). As you type “OT1” into the search box, the auto-filling capability kicks in and you can select the transgene name (see Figure 1).
Figure 1: Autofill options: OT1
When either option is selected, only two strains that actually carry the OT1 transgene are returned in the results. Click on a strain name to open and read the strain data sheet for either strain. If instead you typed in “OT1” and hit the enter key without using the auto-fill options, the search will then look for strains for with the text “OT1” appearing anywhere on their strain datasheet. This search returns more than 10 additional strains that do not express the OT1 transgene but lists the term “OT1” somewhere on their datasheets.
String ‘em together: Searches using word strings.
Searching for mouse models by phenotype or disease term using keyword strings (that is, multiple keywords), in quotes can reduce the number of results returned. For example, if you perform a keyword search for mice with lung cancer-related applications by entering “lung” and “cancer” without quotation marks, the search returns >360 strains in which “lung” and “cancer” appear somewhere—but not necessarily together—on a strain datasheet. By comparison, if you put the phrase “lung cancer” in quotation marks, the search only returns those strains in which “lung cancer” appears as a word string on the datasheet. This list includes only around 60 strains, a much more manageable number (see Figure 2).
Figure 2: Keyword search for individual words vs. word string
Refining Searches: Limiting Frustration!
For some searches, refining your search before you even enter your keywords can improve your search experience, too. The left-hand side of the JAX® Mice Search page lists categories that you can select to limit your search and reduce the number of results. These categories are those that our customers commonly use, including “cre-expression,” “conditional (floxed),” “null/knockout,” “transgenic,” “inbred,” and “reporter (fluorescent),” among others.
For example, if you are looking for an Apoe knockout mouse, check the “Null/Knockout” box to limit your search to only strains with null or knockout mutations. Then start to type “Apoe” into the search box but DO NOT hit “Enter”. From the auto-fill options, you can select “Apoe, apolipoprotein E” as the gene name. This will pull a short list of strains (Figure 3), all of which carry an Apoe null or knockout mutation. Once again, click on a strain name to access that particular strain’s datasheet.
Figure 3: Refining search for null/knockouts and then gene name.
Let’s try another example: Say you are looking for a mouse strain with endothelial cell-specific cre expression, but you’re not sure what genes express in these cells and can’t use a gene symbol to help you to find a mouse. Check the “Cre-expressing” box to limit your search to cre strains. Next, type “endothelial” into the keyword search box, and then hit “Enter” on your keyboard or the magnifying glass at the right hand side of the search box. Our search engine will then return only those strains identified as cre-expressing with the term “endothelial” on their strain datasheets (Figure 4).
Figure 4: Search for cre strains by tissue/organ expression
If your keyword search term is included in the brief strain description, it will be highlighted. If you do not see your keyword, then click on the “SHOW MORE” feature below a strain’s description (Figure 3) to see where on the datasheet the word exists.
Still can’t find your mouse?
If you can’t find the strains you want in The Jackson Laboratory’s Repository, try searching for them in the Mouse Genome Informatics database. If you find them, search the International Mouse Strain Resource (IMSR) to see if they are available from a mouse repository. If they are not available, then you’ll likely need to contact the investigator(s) who made them.
If the mouse model(s) that you need for your research are unavailable or have not even been generated, The Jackson Laboratory offers mouse Model Generation Services that can assist you in generating the mouse models you need using either CRIPSR/Cas9 mutagenesis, transgene microinjection, or ES cell microinjection.