1. TCP LIMS – Mouseline Passports
Objectives
provide TCP users with an understanding of how TCP’s online Mouseline Passport module functions

2. Hands-On Course
This is a hands-on course; users must have LIMS open while navigating through this material to practice what is being demonstrated.
To start, please visit TCP’s DEMONSTRATION site (
All Data contained on this site is not live and will not send any notifications to users.
We recommend using Firefox or Chrome when accessing LIMS. Other browsers (especially Internet Explorer) will work 'most of the time' but they are not supported.

3. Log In
Try It
Log in to the LIMS demo system ( ca)
Use one of the following users to log in
training1, training2, training3, training4
The password for all training accounts is tcp123

4. Mouseline Passports
At TCP, we use mouseline passports to capture genetic and welfare information about a mouseline.
Each mutant mouseline is associated with 1 or more alleles.
Each mutant allele includes sufficient information about the allele to enable users to differentiate the allele from the wild-type allele along with protocols for genotyping.
This is particularly important for genetically engineered alleles and mouselines to meet government regulatory requirements pertaining to genetically engineered organisms and CCAC guidelines.
If published or submitted directly to MGI, alleles can be linked to MGI.

5. Mouseline Passports
Complete and accurate mouseline passports are important because:
They assist TCP and users in complying with CCAC guidelines on the use of animals in research.
They provide facility staff with information that enables optimal care of the animals.
They provide labs using the animals a convenient place to store relevant information about the mouseline enabling current and future lab members to know what they are using and ensure experiments with the mouseline can be accurately reported and reproduced – hallmarks of performing valid and publishable research.

6. Mouseline Passports
If your lab regularly creates new mouselines and/or maintains closed breeding colonies of lines acquired from commercial or academic sources, your PI likely has an ILAR “lab code” (
The lab code is used to denote who created an allele and to identify substrains or sublines maintained in closed breeding colonies. If your PI does not have a lab code, you may want to discuss with your PI whether one is needed.

7. Mouseline Passports
Colonies of the same mouseline that are maintained in separate closed breeding colonies by different labs for more than 5 generations should each have their own mouseline passport.
Independent genetic drift may result in two different sub lines that should not be used interchangeably as the genetic drift may result in different phenotypes and may necessitate using different control animals.
The can be differentiated by using lab codes in the strain name.
If both labs maintain their colonies by crossing to wild-type mice from the same commercial source, the two lines can be considered to be the same as they are not in “closed” colonies.

8. Summary: This panel details the mouseline’s common and official name, which animal use protocols are using it, the number of active cages at TCP for this mouseline, source information, and associated alleles.
Viewing Passports
The Strain Code will be set by our Model Production or Cryopreservation Core if the mouseline is genotyped or cryopreserved at TCP.
The Common Name is the name that will appear on your cages unless you specify a different one to be used for your AUP’s cages.
The common name must uniquely identify the mouseline and may include information about the strain background and/or alleles.
The common name should not include genotype information as this may change over time depending on breeding strategy.
This is especially critical when multiple lab members or labs may be using the same mouseline.
The Official Nomenclature is dictated by the genetic make-up of the mouseline and should follow the naming conventions provided at MGI by the International Committee on Standardized Genetic Nomenclature for Mice.
It is the name that will be used in publications and other public resources.
Please make sure to follow the appropriate naming conventions.

9. Naming Mouseline Passports
When entering the common and official name for the mouseline, you must follow the naming conventions described in the Mouseline >> Mouseline Naming Guide page.
Do not include the genotype in a mouseline name - e.g. Prpl flx/flx or Sybl +/-
Genotypes refer to individual mice, not entire mouselines. While an investigator may decide to maintain a line as a homozygote, that information should not be in the mouseline name.
It can be put in the comments section.
Multiple strains may appropriately appear in the official strain name. This is meant to show the strain background history of a line, e.g.

10. Animal Protocols: This panel lists the animal protocols that have been approved to use this mouseline, the common name that the AUP uses for the mouseline, and the number of active cages in the facility.
Viewing Passports
The number of active cages at TCP provides a quick reference for the number of active cages of a given mouseline on each AUP approved to use that mouseline.
It can also be useful if your group is interested in acquiring a new mouseline because it can save you the time and effort of generating mice if some already exist in the facility.

11. Nomenclatlure: This panel details the mouseline’s origin and background strain details.
Viewing Passports
The Background Strain is the name of mouseline that this mutation was generated in or backcrossed onto.
You can mark a mouseline as confidential if there is a strong reason that the mouseline information cannot be shared with other labs.
This will hide the mouseline from other users and it will not appear in searches of the LIMS database by other LIMS users.
Alleles associated with a confidential mouseline are NOT automatically marked as confidential and vice versa.
There is no obligation to share mice just because a mouseline is visible on LIMS.
Advantages of allowing passports to be viewed by all LIMS users is that it can open opportunities for new collaborations.

12. Allele: This panel lists the alleles associated with the mouseline.
Viewing Passports
The order of the alleles determines the order that the alleles will appear on the cage card.

13. Welfare: This tab shows any known welfare issues common to the mouseline including the number of mice that have exhibited the phenotype associated with the welfare issue.
Viewing Passports
When you initially create the mouseline, if you do not suspect that there will be any welfare concerns, select ‘New Mouseline, Welfare Concerns Unknown’.
Once you have established a colony, you should update the welfare tab with ‘No Welfare Concerns’ or ‘Identified Welfare Concerns’ (with the specified concerns).
Assessment of welfare for genetically engineered animals is particularly important as the genetic modification may cause a phenotype that compromises mouse welfare, such as tumour burdens that affect health and well-being, anemia or immune deficiencies that require special handling of mice or shorten life span, morphological changes that affect abilities to feed or obtain water in standard caging, etc.
By identifying welfare issues, intervention of veterinary staff can be minimized and/or anticipated so as not to negatively affect planned experiments.

14. Attachments: This tab allows you attach files related to the mouseline
Attachments: This tab allows you attach files related to the mouseline. You can also access any attachments for the mouseline’s alleles.
Viewing Passports

15. Actions: This panel provides convenient links for working with Mouseline Passports.
Viewing Passports
The Get PDF link can be used to generate a PDF that includes all the information about the mouseline and its alleles.
The Clone link can be used to make a copy of the mouseline. This copy will have the same alleles and welfares associated with it.
The Combine link can be used to combine the details of the mousseline you are viewing with another mouseline.
The Create Amendment link will navigate to the Mouseline Amendment page so that you can request to add the mouseline to your AUP.

16. Actions: This panel provides convenient links for working with Mouseline Passports.
Viewing Passports
The View Mice link will redirect the user to the Mouse Search page and display all mice that express this mouseline.
The Similar Mouselines area in the Action panel can be used to find other mouselines in LIMS that use the same alleles as this mouseline.

17. Summary: This tab details the allele’s official name, symbol, and short form, who created it, and a description of the mutation.
Viewing Alleles
The genetic modification type refers to the way the allele was made and includes spontaneous alleles.
In general, alleles in so- called wild-type strains (e.g. ICR, CD-1, C57BL/6, etc.) do not need to be added to mousselines of those strain backgrounds.
However, if an allele from one strain is backcrossed into another strain background or spontaneously arises in a strain background, it should be indicated as an allele.
The Allele Name and Allele Symbol are the name and symbol that will be used in publications and other resources.
The Short Form is the name that will appear on cage cards. This is limited to 6 characters and must be unique.
Please make sure to follow the naming conventions for alleles provided at MGI by the International Committee on Standardized Genetic Nomenclature for Mice.

18. Summary: This tab details the allele’s official name, symbol, and short form, who created it, and a description of the mutation.
Viewing Alleles
You can mark an allele as confidential.
Confidential alleles will not appear in searches by other users of LIMS.
Only users on AUPs approved to use the mouseline associated with the allele are able to view confidential alleles.
Published alleles (publicly viewable in MGI) should never be marked confidential. Mouselines that use confidential alleles are NOT automatically marked as confidential.

19. Summary: This tab details the allele’s official name, symbol, and short form, who created it, and a description of the mutation.
Viewing Alleles
Original strain background refers to the strain in which the mutation was originally made or in which it spontaneously arose.
When the original strain for the allele is different from the mouseline strain background, it is often the case that there are other genes/alleles linked to the indicated allele that are from the original source.
This can be important when interpreting phenotyping or other experimental results.

20. Details: The information on the Details tab changes depending on the “genetic modification type” selected on the summary tab.
Viewing Alleles

21. MGI: The information on the MGI tab links the allele to published alleles on MGI.
Viewing Alleles
If the gene and allele are in MGI, add a link to the appropriate entries.

22. Genotyping: This tab allows labs to record their method for genotyping the allele.
Viewing Alleles

23. Attachments: This tab allows you attach files related to the allele.
Viewing Alleles

24. Mouseline Passports – A Recap
At TCP, we use mouseline passports to capture genetic and welfare information about a mouseline.
Each mutant mouseline is associated with 1 or more alleles.
Each mutant allele includes sufficient information about the allele to enable users to differentiate the allele from the wild-type allele along with protocols for genotyping.
This is particularly important for genetically engineered alleles and mouselines to meet government regulatory requirements pertaining to genetically engineered organisms and CCAC guidelines.

25. Mouseline Passports - A
Complete and accurate mouseline passports are important because:
They assist TCP and users in complying with CCAC guidelines on the use of animals in research.
They provide facility staff with information that enables optimal care of the animals.
They provide labs using the animals a convenient place to store relevant information about the mouseline enabling current and future lab members to know what they are using and ensure experiments with the mouseline can be accurately reported and reproduced – hallmarks of performing valid and publishable research.

26. Mouseline Passports – A Recap
The common name must uniquely identify the mouseline and may include information about the strain background and/or alleles. The common name should not include genotype information as this may change over time depending on breeding strategy.
The Official Nomenclature is dictated by the genetic make-up of the mouseline and should follow the naming conventions provided at MGI by the International Committee on Standardized Genetic Nomenclature for Mice.
The Background Strain is the name of mouseline that this mutation was generated in or backcrossed onto.

27. Alleles – A Recap
The Allele Name and Allele Symbol are the name and symbol that will be used in publications and other resources. Please make sure to follow the naming conventions for alleles provided at MGI by the International Committee on Standardized Genetic Nomenclature for Mice.
Original strain background refers to the strain in which the mutation was originally made or in which it spontaneously arose.

28. Mouseline Passports
Try to use existing mouselines. New Mouselines should be created if you are
importing new line into TCP, or
creating new line for experimentation. A new line may be created on your behalf at the Model Production Core, imported from an external commercial or academic source, or result from intercrossing different mouselines or backcrossing alleles onto different genetic backgrounds.

29. Allele Search
To search for existing alleles, navigate to Mouseline >> Allele Search.

30. Allele Search
To search for existing alleles, navigate to Mouseline >> Allele Search.
Before creating an allele for a mouseline, search existing alleles in LIMS to make sure it is not already in LIMS. If it already exists, it will save you time.

31. Mouseline Search
To search for existing alleles, navigate to Mouseline >> Mouseline Search.

32. Creating and Editing Mouseline Passports
When creating a new mouseline passport
All fields in all tabs should be completed, especially MGI links and genotyping information.
Mouselines should be reviewed as part of the AUP’s annual renewal to ensure that the information on it, especially the Welfare information, is correct.

33. Creating and Editing Mouseline Passports
To create a new mouseline passport, you can:
1. clone an existing mouseline passport and make minor modifications
2. combine existing mouselines passport. This mouseline passport will have all the alleles and welfare issues associated with the source mouselines selected during the combine process
3. create a new mouseline passport

34. Combining Mouseline Passports
If you are breeding mice from 2 existing mouselines with each other, the easiest way to create the new mouseline passport in LIMS is to use the Combine feature.
The fields of the new mouseline will be a combination of the information from each originating mouseline.

35. Log In
This is a hands-on course; users must have LIMS open while navigating through this material to practice what is being demonstrated.
To start, please visit TCP’s DEMONSTRATION site (
All Data contained on this site is not live and will not send any notifications to users.
We recommend using Firefox or Chrome when accessing LIMS. Other browsers (especially Internet Explorer) will work 'most of the time' but they are not supported.
Try It
Log in to the LIMS demo system ( ca)
Use one of the following users to log in
training1, training2, training3, training4
The password for all training accounts is tcp123

36. Combining Mouseline Passports
Try It
Navigate to the View Mouseline page for the Blue mouseline passport.
Combine the Blue mouseline passport with the Red mouseline passport to create a Purple mouseline passport with the name “Purple - <your name>”
You will needs to the Mouseline Passport PDF to the to pass this course

37. Cloning Mouseline Passports
The clone feature can be used if
the same experiment has produced several different alleles of the same gene and all the information for the mouseline, except the allele is the same
the mouseline is made by modification of an allele, e.g. Cre or Flp treatment, so that all the information except the allele is the same.
you are backcrossing a mouseline to get the allele(s) onto a different genetic background. All the information about the mouseline, including the allele, is the same except for the strain background.
Be aware that if the original mouseline has alleles associated with it, the cloned mouseline will have the same alleles on it (and not copies). Any changes to the alleles on the cloned mouseline will also affect the original mouseline.

38. Combining Mouseline Passports
Try It
Navigate to the View Mouseline page for the Red mouseline passport.
Clone the Red mouseline passport to create a Cre version of the mouseline passport with the name “Red.Cre - <your name>”
Add the Cre allele
You will needs to the Mouseline Passport PDF to the to pass this course

39. New Mouseline Passports
The passport will not be added to your animal use protocol until an amendment is submitted and approved.

40. TCP LIMS The live site is available at https://lims.phenogenomics.ca.
Questions
Contact the LIMS Team at