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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?
- Open a web browser and go to
https://lims2.phenogenomics.ca
- Click on 'Register New User'
- 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.
- 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.
- 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.
- 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.
- 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.
- To search, go to Mouselines > Search Mouseline
- 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.
- 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.
- Navigate to Mouselines > New Mouseline Passport.
- Click Continue.
- On Step 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
- 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.
- 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.
- On Step 2:
- 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.
- 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.
- Select Subtype
- On Step 3:
- 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))
- 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.
- 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
- 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.
- On Step 4:
- 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.
- 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"
- Click Next.
- On Step 5:
- 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:
- 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.
- On the right hand side, in the box marked
"Actions", click "Combine ..."
- 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.
- Click Continue
- Step 1: Follow the instructions for Step 1.
- Step 2: Follow the instructions for Step 2.
- 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.
- Step 4: Follow the instructions for Step 4.
- 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.
- Navigate to AUPs > ACC Documents > Amendments.
- Select the AUP
- Open the Mouseline panel and select Yes for the Changes option.
- Select the mouseline you wish to
add
- 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.
- 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.
- 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?
- Navigate to AUPs > ACC Documents > Amendments.
- Select the AUP
- Open the Personnel panel and select Yes for the Changes option.
- Select the person you wish to
add.
- 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.
- 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 Protocols service
request is required.
- Navigate to Service Requests > Facility > Transfer
Between Protocols.
- 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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