1. TCP LIMS – Cage Cards II Objectives
demonstrate how TCP users can work with cages using our Laboratory Information Management System (LIMS)

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. Setup Breeding Cages
The Setup Breeding page can be used to set up cages with matings.
To get to the Setup Breeding page, you can
View a Cage and click the Setup Breeding link from the Actions panel
Navigate to Cage >> Cage Actions >> Setup Breeding from the menu
Navigate to Cage >> Cage Search, select the cages containing the mice you wish to mate, and click Setup Breeding from the Actions panel
The litters that are produced by the breeding pair are automatically assigned the cage's mouseline.

5. Setup Breeding Cages
Additional cages are added using the Scan Barcode field.
Click the Select button for 1 male mouse and 1 or 2 females.
If the wrong mouse is selected, click the Unselect button on the Breeding cage.
Fill in the fields with red asterisks (*)
Click Save

6. Setup Breeding Cages
You can create multiple breeding cages and the list of created cages is displayed at the top of the page.
Try It
Set up a Breeding Cage.
Add the cage to the Holding Area (for the next step).
Save the cage card PDF for the cage.
You will need to the cage card to the to pass this course
On the production system, you would print the new cage cards for all modified cages.

7. Adding Litters
When a breeding pair produce a litter, the litter needs to be added to LIMS before the pups can be weaned.
Try It
Add a Litter to the Breeding cage you created in the previous step.
Set the number of females to 5 and number of males to 6
For this exercise, enter the date 21 days ago as the birth date.
Click the Save button.
If the pups are too young to determine their sex, enter the total pups born.
The staff check for litters every other day. If the exact date of birth is important to you, you must check the cage every day.

8. Scheduled Weanings
The Home Page displays all of your scheduled weanings.
The scheduled wean date is 21 days from DOB. If users do not wean their litters within 2 days of the scheduled wean date, the staff will wean the litter and charge the lab for these are unscheduled weanings.

9. Culling Litters If you choose to cull a litter instead of weaning it,
navigate to the View Cage page.
Set the litter’s Weaning Status to Not Weaned.
Set the Other Pups Status to indicate why the litter was not weaned.
These include Sacrificed, Eaten, Dissected, and Found Dead.

10. Weaning Litters To get to the Wean Cages page, you can
View a Cage with an active litter and click the Wean link from the Actions panel
Navigate to Cage >> Cage Actions >> Wean Cages from the menu and then enter the cages you wish to wean
Navigate to Cage >> Cage Search, select the cages containing the mice you wish to wean, and click Wean Cages from the Actions panel
Additional cages are added using the Scan Barcode field.
Select the litters you wish to wean and enter the total number of males and females.
Click the Next button.
Include the animals you plan to cull in the number of males and females. Doing so will allow you to track the fertility and viability of your mouseline.

11. Weaning Litters
The Allocate Mice screen allows you to put the weaned mice into cages.
Basic Weaning
Cull Mice - Click the small x beside the checkbox.
Allocate Mice - Click the Allocate Mice button at the bottom of the page
Click the Next button.

12. Weaning Litters
You can edit any of the cage card fields (such as genotyping) by clicking the Edit button at the top right of the cage card.
After you have finished editing the card, click the Save button to save your changes.
On the production system, you would print the new cage cards for all new cages.

13. Weaning Litters
The Allocate Mice screen has many features which we shall explain now.
Numbering Mice
Mice can be auto-numbered based on
the source or destination cage
with a specified start value
with a specified increment value
sex
Culling Mice
Individual - Click the small x beside the checkbox.
By Sex – Check the M or F option and click the Cull Mice button.
Culled mice do not count towards your protocol’s animal usage.

14. Weaning Litters Allocating Mice Options include pooling litters
if weaning more than one cage at a time
maximum number of mice in a cage
equal distribution within cages
for example, if there are 7 females, an equal distribution would be 4 and 3 mice per cage as opposed to 5 and 2
Weaned mice can also be moved into existing Stock cages.
In the Destination Panel, you can scan in cages or import held cages for existing destination cages.
Once the cages are displayed, you can drag and drop mice from the litters into the appropriate destination cages.

15. Weaning Litters Each mouse’s genotype can be recorded before weaning.
Recording Genotype
Enable the Show Genotyping option
Set the allele zygosity based on the results you have received
Click the Update Mouseline button, to have the system update each mouse’s expressed mousseline.
Setting the mouse’s mouseline will affect the destination cage that mouse is allocated to.

16. Weaning Litters Cage Options
You can set some cage fields before generating the cages using the Cage Options dialog.
These values are set for any cages created after the options are set.

17. If you always use the same weaning options, click the Weaning Preferences link at the top right of the page and save your preferences.
Weaning Litters
You can then use the Quick Wean option on the first page of the weaning process.

18. Weaning Litters
Try It
Navigate to the Breeding cage you created in the previous step.
Wean the litter.
Cull at least one pup.
Number the females ‘N1-’ with odd numbers
Number the males ‘N1-’ with even numbers
Record the genotype for some of the pups.
For Males, set the cage maximum to 2.
For Females, set the cage maximum to 3.
Save the cage card PDF for the cages.
You will need to the cage card to the to pass this course

19. Managing Genotypes To get to the Manage Genotypes page, you can
The Manage Genotypes page allows users to enter genotypes on the alleles for all the mice in the cage.
To get to the Manage Genotypes page, you can
View a Cage and click the Manage Genotypes link from the Actions panel
Navigate to Cage >> Cage Search, select the cages you want to update, and click Manage Genotypes from the Actions panel
Set the allele zygosity based on the results you have received.
Select the assay used to determine the zygosity.
Next, click the Update Mouseline button, to have the system update each mouse’s expressed mousseline.

20. Move Mice To get to the Move Mice page, you can
When moving mice, each cage can only contain mice of the same sex (unless it is a Breeding Cage or Stud Cage), same mouseline, and be part of the same AUP.
To get to the Move Mice page, you can
View a Cage and click the Move Mice link from the Actions panel
Navigate to Cage >> Cage Actions >> Move Mice from the menu
Navigate to Cage >> Cage Search, select the cages you want to update, and click Move Mice from the Actions panel

21. Move Mice Additional cages are added using the Scan Barcode field.
To move an individual mouse, click on a mouse and drag it to the destination cage or the Terminate Mouse panel.
To create a new cage, specify the cage type and drag a mouse to the Create Cage panel.
To move all of the mice in a cage, click on the cage label and drag it to the destination cage or the Terminate Mouse panel.
To terminate a mouse, drag the mouse to the Terminate Mouse panel.

22. Terminating Cages To terminate a cage, you can
View a Cage and click the Terminate link from the Actions panel
Navigate to Cage >> Cage Search, select the cages you want to update, and click Terminate from the Actions panel
The following pop-up will appear.
Enter the Reason for termination and the Method, and click Save.
Users must terminate cages that are no longer needed, otherwise the cage continues to get charged to the lab for up to 45 days from the day it is last scanned. Cages are scanned regularly by staff to keep them active in the system.

23. Terminating Cages To terminate multiple cages, you can
Do not terminate cages until they are removed from the racks. If the staff scans a terminated cage, LIMS will automatically unterminated it and the lab will continue to be charged per diems.
To terminate multiple cages, you can
Navigate to Cage >> Cage Actions >> Terminate Cages
Enter the Reason and the Method.
Scan in the barcode from the cage cards.
Click Terminate.

24. TCP LIMS The live site is available at https://lims.phenogenomics.ca.
Questions
Contact the LIMS Team at
Using the live system ( download the SOP that covers ‘Cage Card Creation and Termination’ on LIMS and read it.