10/17/98

Gary E. Truett

Pennington Biomedical Research Center

truettge@mhs.pbrc.edu

We use two files for mouse colony management, Mice.fm and MiceDams.fm.

1) Mice.fm is the main file.

A. Layouts

status is the main layout. This layout includes most of the fields.

new animals is used by the new litter button. When a new litter is entered the new records are listed in this layout.

Unmarked is used by the find unmarked button. This button generates a list of mice that have "Y" in the live field and "mark" in the marks field.

Genotype me is used by the find ungenotyped mice. This button generates a list of mice that have "Y" in the live field and "genotype" in the geno field.

Card labels is used to create 1" by 4" labels for cards for individual animals.

Pedigree list is useful for generating pedigree files. Pedigree files begin with the mouse id followed by the dam id and the sire id. They are used in other applications to generate pedigree trees.

B. Fields

id is incremented by 1 for each new record. To reset the id number, select file, define fields, id, options, and enter the next value in the appropriate box.

Litter is incremented by 1 when you enter a new litter.

Dam is the id for the dam of the mouse. The dam field is filled when you enter a new litter.

sire is the id for the sire of the mouse. The sire field is filled when you enter a new litter.

Born is the date of birth. When you enter a new litter, the current date is automatically assigned as the date of birth. You can change the data manually if the current date is not the date of birth.

Weaned is the date to be weaned. The default value is calculated as the date of birth plus 24 days. You can reset the default value

killed is the date killed. The kill me and kill all buttons assign the current date to this field.

sibs is the number of mice in the litter. The number of sibs is entered when you enter a new litter.

Strain is the strain code. You can define the strain codes in layout mode. Highlight the strain field.

Sex is either "M" or "F". We usually assign the sex codes when we mark the mice.

geno is the genotype. We use 0, 1 and 2 as our genotype codes. The default value "genotype" is assigned when you enter new animals. If you wish to use other codes, define the codes in the value list for the field. Go to layout mode. Highlight the geno field. Select field format from the format menu. Highlight the box after using value lists and select "Define value lists". Enter your codes in the geno value list.

mark is a marking code used to distinguish among littermates.

F is the generation code, such as F1, F2, N2, etc. This field is marked when a new litter is entered.

experiment is used to name the experiment the mouse is assigned to.

notes is used for comments.

pheno is used for simply phenotype descriptions such as lean and obese. We actually use this very little. Most phenotypic values are entered in related files generated for each experiment.

live is either "Y" or "N". This field is used frequently when sorting. When a new mouse record is created, live ir set to "Y". The "kill me" and "kill all" buttons set this to "N".

status is used to track the

breeder is marked "Y" by the breed button. We use this occasionally to select the breeder records for exporting. You probably won’t use this much.

count is used when generating records for new litters. Don’t enter anything in this field.

room holds a room id.

protocol holds an Institutional Animal Care and Use Committee protocol number.

 

C. Buttons

Status layout

kill me changes the status of the current record to "dead", enters the current date in the killed field, and changes the live field to "N".

kill all changes the status of all records in the browse list to "dead", enters the current date in the killed field, and changes the live field to "N".

DAMS opens the MiceDams.fm file.

Find enters find mode.

Close closes the file.

Zip backup backs up Mice.fm and MiceDams.fm to a zip disk. The script assigned to this button is titled "zip backup both mice and micedams".

Find live searches for all mice with "Y" in the live field.

Find pregnant searches for all mice with "pregnant " in the status field.

Find nursing searches for all mice with "nursing " in the status field.

Find unweaned searches for all mice with "neonate " in the status field.

Find unmarked searches for all mice with "mark " in the marks field. The results are displayed in the unmarked layout.

Find ungenotyped searches for all mice with "genotype" in the geno field. The results are displayed in the Genotype me layout.

Breed opens the MiceDams.fm file and waits for you to enter a Dam id. Enter the dam id and press continue. Breeding records for that dam are then retrieved and a new breeding record is created with the current date in the in field and"breeding" in her status field. The script pauses to allow you to enter the id of her mate. Enter the mate id and press the continue button. The status of her mate is changes to breeding.

Unbreed opens the MiceDams.fm file and waits for you to enter a Dam id. Enter the dam id and press continue. Breeding records for that dam are then retrieved. Status of the dam is changed to pregnant, and the current date is pasted into the out field. Press the continue button and the status of her mate is changed to "waiting to breed".

New litter opens the MiceDams.fm file and waits for you to enter a Dam id. Enter the dam id and press continue. Breeding records for that dam are then retrieved. Press continue. A list of all litters in MiceDams.fm is displayed. Scroll to the bottom and highlight the last litter id in the list. Press the paste button. The litter id is pasted into the lit id field and incremented by 1. Enter the number of pups in the sibs field. Press continue. Enter the Generation code in the Gen field. Press continue. A message reminds you to check all filed before proceeding. Press continue. Review the fields and make any corrections. Press continue. A message " Create new records?" appears. Press Yes. New records are created in the Mice.fm file for the new mice. The animals are listed in the New Animals layout.

Wean all enters the current date in the weaned field and changes the status to "weaned".

New Animals layout

Kill me changes the status of the current record to "dead", enters the current date in the killed field, and changes the live field to "N". We use this button on the New Animals layout to note which new mice were born dead.

New litter performs the same function as the new litter button on the status layout.

DAMS opens the MiceDams.fm file.

Status returns to the status layout.

Unmarked layout

Find unmarked searches for all mice with "mark " in the marks field.

Enter marks automates entry of marking codes for a litter. The script pauses to allow you to enter a litter id. Enter the litter id and press continue. A message tells you to press the MARK button to enter marks. The marks are entered for each mouse in the litter. The marking codes we use are for toes marks. We marks our mice during the first week of life and use the toes to genotype them. The codes are for the outermost toe on each paw. RF=right front, RB= right back, LF=left front, and LB=left back. Combinations of toes are used to mark more than 4 per litter. If you want to changes the codes, edit the "enter marks" script.

DAMS opens the MiceDams.fm file.

Status returns to the status layout.

2) MiceDams.fm

A. Fields

mate is the id of the male in the breeding pair.

In is the date the breeding pair is set up.

Out is the date the male is removed.

lit id is the id of the new litter.

Sibs is the number of pups in the new litter.

Gen is the Generation code of the new litter; F1, F2, N2, etc.

B. Buttons

Find a dam’s breeding history finds all breeding records for a particular dam.

The remaining buttons perform the same tasks described above for Mice.fm.