How To

How do I ...

How do I make a suggestion for an improvement?

If you have an idea for an improvement to LIMS, please let us know.

Click on the Bug Report link and describe your idea. The link is at the bottom of every page.

How do I register for a LIMS account?

  1. Open a web browser and go to https://lims2.phenogenomics.ca
  2. Click on 'Register New User'
  3. Follow the steps to register ensuring that every field with a red asterisk is filled. Your account password will be e-mailed to the address you provide during the registration process.

How do I get training at TCP?

Anyone who wants access to TCP unsupervised MUST complete all 4 training courses and be listed on an AUP to access the facility and handle live mice. If a person is only going to observe on the rare occasion they can be signed in as a guest but this person has to be signed in to the facility with Betty-Jo's permission and supervised at all times. If the person is to observe more frequently (say, once per month) then they should go through the training procedures. See SOP SEC005 for details.

  1. Have the new user go to LIMS, click on "New User" and sign up, under the lab that will be responsible for them. Within the week the person will be approved (if there are issues, speak with Julia Silva, ACC Co-ordinator) and an email will be sent to the user with a password.
  2. Once the new user has a password, have them log into LIMS, go to Facility > Training, and click on the Enroll button for the courses they need to take. Courses are free of charge but if the user signs up and misses the training session then the lab is charged a $50 no show fee. All users must sign up for the following courses:
    • Building Orientation & Safety - This course is mandatory for new users who will require access to the animal facility. It includes general orientation to the building, security and emergency responses, fire safety, occupational health and safety and incident reporting.
    • Regulatory Oversight & Animal Ethics - This online course is mandatory for new users who will require access to the animal facility. It includes an overview about guidelines, legislation and regulations for using animals in research in Canada, ethics in animal experimentation and the Three Rs of humane animal experimentation. .
    • LIMS Colony Management- This self-directed, online course a 2 hour course that gives an overview of the functionality of LIMS.
    • Laboratory Safety Training (aka WHMIS) - unless the user can show WHMIS training within the year, they need to go to this course. The course is taught by Cynthia Pressman. If the new user enrolls when they are new to the lab, then it is covered.
    • Colony Management & Mouse Handling - This course is mandatory for new users who will require access to the animal facility. A PowerPoint presentation will introduce concepts related to mouse colony management. Hands-on instruction will be provided for mouse handling, monitoring, mouse identification, injection techniques, oral gavage, blood collection and euthanasia.
    • Euthanasia of Experimental Animals - This course is mandatory for new users who will require access to the animal facility. It includes the principles of euthanasia, criteria for humane techniques, advantages and disadvantages of the various methods of euthanasia, and the euthanasia services offered from the TCP technical services.
  3. At the General orientation session, the user is given the TCP facility access card form (can also be found on LIMS at Request for TCP Animal Facility Access Card Once they complete the training sessions, hand the form to your lab's administrator.
  4. On the form there is a section that asks for the AUPs the person will be on. Based on the user's project, the lab administrator will list which AUPs the user will work on and request which TCP building levels the person should have access to (F1, F2, etc). The user must be added to the relevant AUPs on LIMS. The new user will only have access to the mice on that AUP. (See how to add someone to an AUP?)

Users must be given a copy of the AUP that they are on, including the Hazardous Agents response forms and SDS sheets for any chemicals / toxins / biological agents that are permitted. Only mice that are actually listed on that AUP on that cage card (rather than listed as a mouseline) are allowed to undergo procedures listed on that AUP. See the instructions on how to transfer cages to a different AUP.

How do I find an existing mouseline?

Often, a researcher at TCP already has your mouseline in question.

  1. To search, go to Mouselines > Search Mouseline
  2. Note the default on searching is "mouselines on my cages" in the light brown box. Unclick this to see all of what TCP may have in inventory. You can search by keyword or MGI gene / allele.
  3. If a mouseline of interest is there, note the PI. If there are no PIs listed then it is unlikely the mouse is alive in the facility, but if several are listed, you may be able to contact them to see if they have it alive. Try to find someone with the mouse alive on F1 as then the mouse can travel to F2, but not the other way around (SLRI and SickKids researchers are a good bet). You can also click on the mouseline and have a look at who is the point of contact.

How do I create a mouseline passport for a new allele?

A mouseline passport is essentially an identity card for the mouseline. It lists the alleles, the background, and the contact information of a particular line. If you are generating a new allele, then this needs a new passport. TG Core cannot proceed without a valid mouseline for the mouse.

  1. Navigate to Mouselines > New Mouseline Passport.
  2. Click Continue.
  3. On Step 1:
    1. Name for the new passport: this will appear on the cage card in the mouseline box. Keep it short yet descriptive (such as Ins2-cre;ROSArtTA(n-in);TetO-OSKM). The name can be a maximum of 32 characters long so keep this in mind if there are multiple alleles. Separate alleles by semicolons (;).
      • If the mouseline is definitely one specific background (or you are backcrossing), use a short form for the background prior to describing the alleles so as to keep it distinct (129.Oct4-GFP vs. B6.Oct4-GFP). Add a period (.) after the background to denote background and not an allele
      • if a mouse comes directly from Jax, then TCP likes the stock number as part of the name for the new passport : TNAP-Cre / J#08569
    2. Official nomenclature for this strain: Here you can be more descriptive of the mouseline. If it is a single allele, then its best that you use the MGI strain name (such as STOCK Tg(CMV-GFP)1Nagy for B5/EGFP) . If you are creating a new cross, then you have the space to write the alleles out in full (STOCK Gt(ROSA)26Sortm1(rtTA*M2)Jae Col1a1tm3(tetO-Pou5f1,-Sox2,-Klf4,-Myc)Jae/J for ROSArtTA-M2; Col1-TetO-OSKM). It is best if you can name it in formal MGI style but that requires a deeper understanding of nomenclature. Lauryl has helped me with this before, especially when I was asking her to freeze a line for me.
    3. Additional comments: if you are making a new single allele transgenic, it is best to describe how the ES cells were made and any notes about the generation of the mouse. If you are crossing multiple alleles, I find it best to create a full description of how you did the cross (including adding backgrounds if you are creating a mixed background and where you got the mice from). This helps with tracking down the road.
  4. On Step 2:
    1. Select the Strain Type: if you are making a novel single allele transgenic, select Mutant Strain. If you are making a new cross, select Mutant Stock.
    2. Enter Background strain: if you know it, great, if not, you can use "Unknown" or "Mixed". If you used G4 ES cells, then use the appropriate cross.
    3. Select Subtype
  5. On Step 3:
    1. At this point you have the option of choosing existing alleles or creating a new allele that the TG Core has generated for you. I will use an example of adding a new allele to an existing mouseline (new allele to ROSA rtTA (neo-out))
    2. To find an existing allele, type in the allele as best as you can (ROSA rtTA) and choose the one that best fits your purposes. Some alleles are represented more than once (a relic of the previous system where people added alleles on their own, thus ROSA especially has multiple versions), its best to work off a copy of the allele you know and trust (like one we already have on a passport).
      • You can add the alleles now or after saving the mouseline.
    3. To make an new allele, hit that button. If you think that the MGI database will be of some help to you (if you have targeted a gene, rather than random integration), then find the gene in question (the allele won't be there because you haven't made it yet!). If not, enter the information manually.
      • Fill out the form as best as you can, the more information the better. Here TCP would prefer a MGI based name for the allele, do your best to be as accurate as possible. There are guides online as to how to properly name an allele.
      • The short form is the 6 digit code that will be above the genotyping information. Write here what you will be genotyping for (For example: RrtTA, cre, LacZ, InsKO, etc)
      • If this is a novel allele, it is best if you mark this as confidential.
      • It is best to describe how this allele was generated, the plasmid/knock in/out strategy, the ES cells used, and the media. Anything is useful here. This can also be added when you go to the "Additional Information" page
      • Fill in genotyping information as best as you can from the additional information page
    4. Once the new allele is saved, then you will go back to the allele list page. Make sure that the alleles are in the order in which they function in the cell (cre, then rtta then TetO. etc). This helps with the organization of the mouseline in general.
  6. On Step 4:
    1. If you know that there may be welfare issues with this mouse, then enter it here (tumours, seizures, any issues at all). This will be helpful to TCP staff when/if they encounter a sick mouse. The LIMS will track welfare issues when they are encountered and entered by TCP staff.
    2. If there are no known welfare issues with these mice, then confirm that by clicking the checkbox beside "Confirm that this mouseline has no welfare issues"
    3. Click Next.
  7. On Step 5:
    1. Click save.
Making this mouseline will not add it automatically to the AUP. After saving the mouseline, click the "Create an Amendment" button. This will take you to the amendment page where the mouseline is already filled out, you have to add the AUP and the justification. See how to add a mouseline to an AUP? for instructions.

How do I create a mouseline passport when combining 2 existing mouselines?

A mouseline passport is essentially an identity card for the mouseline. It lists the alleles, the background, and the contact information of a particular line. If all the alleles that you want to cross already exist on LIMS, and the mice are alive in TCP, then the job is a simple one especially if the passports are up to date. The easiest way to accomplish this is to do the following:

  1. Navigate to Mouselines > Search Mouselines and search for your first allele (For exampe: aP2-cre) and then click on the View link to get to the passport.
  2. On the right hand side, in the box marked "Actions", click "Combine ..."
  3. Type in the mouseline you wish to cross with, such as B6.ROSArtTA(neo-in);TetO-OSKM
    • Note: this is a mouseline, not an allele, which means that you will be crossing existing mice that are on your AUPs. You can even combine double transgenics if they exist in the facility. If not, you can combine three individual alleles.
  4. Click Continue
  5. Step 1: Follow the instructions for Step 1.
  6. Step 2: Follow the instructions for Step 2.
  7. Step 3: Make sure the alleles are in the correct order for their action within the cell and genotyping by moving up and down (right hand side). Click Next.
  8. Step 4: Follow the instructions for Step 4.
  9. Click Save and Finish.
Making this mouseline will not add it automatically to the AUP. After saving the mouseline, click the "Create an Amendment" button. This will take you to the amendment page where the mouseline is already filled out, you have to add the AUP and the justification. See how to add a mouseline to an AUP? for instructions.

How do I add a mouseline to an AUP?

Mouselines can only be added if the passport has been created. If no passport has been created, it can not be chosen from the drop down menu. See how to create a mouseline passport for instructions.

  1. Navigate to AUPs > ACC Documents > Amendments.
  2. Select the AUP
  3. Open the Mouseline panel and select Yes for the Changes option.
  4. Select the mouseline you wish to add
  5. For each mouseline you need to provide a justification as to why you need to add the line to the AUP. Be direct and short. If you are adding a single allele transgenic, just tell them why this one is necessary. If you are adding a new cross, let them know why this one is better or different than the others. Also mention that all procedures that are intended for this new mouseline are already approved on the AUP (assuming that this is true).
    • For example: We wish to add ap2-cre;ROSArtTA(n-in);TetO-OSKM. This mouseline is different from the Ins2-cre;ROSArtTA(n-in);TetO-OSKM as we wish to study reprogramming in the context of adipose tissue, instead of the pancreas, where Ins2-cre is expressed. All procedures that are planned for this mouseline are already approved on the AUP.
  6. When adding a mouseline, you have the option of adding to the mouse budget. It is a good idea to slowly increase the budget as you add lines because it is a big pain if you run out of mice before the renewal. Try estimate how many breeders you will need per line, how many litters will be kept per Breeding Pair (BP), and how long you will need these for.
    • For example: we anticipate needing 2 breeders to establish the line and provide requisite mice for the experiments. 2 BP x 10 mice per litter x 6 months = 120 mice added to the AUP.
  7. Click Save.
The changes will be visible once the amendment is approved. This functionality is available to AUP managers and does not require the PI's signature.

How do I add someone to an AUP?

  1. Navigate to AUPs > ACC Documents > Amendments.
  2. Select the AUP
  3. Open the Personnel panel and select Yes for the Changes option.
  4. Select the person you wish to add.
  5. To the right of the personnel selection, you will get a list of check boxes, click all that this person will do (be familiar with the AUP before you do this). TCP will check the training of the person against the procedures you have selected. For instance, if you have selected surgical procedures, they will make sure the person has done surgical training. If not, they will send an email to you and the person to request a scheduling of training.
    • Be aware that the use of the irradiator and the CL2 suite is on this list. Very few AUPs have these procedures and few of us are trained so don't click all boxes.
  6. Click Save.
The changes will be visible once the amendment is approved. This functionality is available to AUP managers and does not require the PI's signature.

How do I change the expressed mouseline of a mouse?

If you discover that your mouse's expressed mouseline is different than you originally assigned it, go to the View Mouse paged and change the value in the expressed mouseline field. You can also change the mouseline for the cage by going to the View Cage page and changing the value in the mouseline field.

How do I transfer cages to a different AUP?

Only mice that are actually listed on that AUP on that cage card (rather than listed as a mouseline) are allowed to undergo procedures listed on that AUP. If a mouse needs to be transferred from one AUP to another then the cage should be moved to the new AUP (as long as the mouseline is common to both). This can only be done by TCP staff and not us, a Transfer Between Projects service request is required.

  • Navigate to Service Requests > Facility > Transfer Between Projects.
  • Fill in the request, and Submit it

How do I change the sex of a mouse?

If you discover that your mouse's sex is different than you originally assigned it, go to the View Mouse page and change the value in the sex field for the mouse. Then go to the View Cage page and change the value of the sex field for the cage.

How do I automatically number my mice?

You can automatically number your mice on the weaning page. See how to assign mice to cages when weaning.

How do I report a bug?

If you experience a problem while using LIMS, please let us know. If you don't tell us about the problems, we can't fix them.

Click on the Bug Report link and fill in the information. The link is at the bottom of every page.


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