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The Mouse Brain Library

Phenotypes of Major Recombinant Inbred Strains

Table of Mouse Strains @ the MBL

Brain Weights of Strains of Mice @ the MBL

Brain Weight Database for Individual Mice @ the MBL

Strain Variation in Retinal Ganglion Cell Number

Individual Counts of Retinal Ganglion Cell Number

Olfactory Bulb Weight Data

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 Mouse Phenome Databases & Mouse Colony Programs

The Mouse Brain Library @ the MBL

Browse or search the Mouse Brain Library (MBL). The library contains high resolutions images (3060 x 2036 pixels, 25 µm per pixel) of individual slides, usually two per case. We are in the process of acquiring images for more than 1500 cases, usually 8 cases per strain cut in either the horizontal or coronal planes. All sections are currently&m&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&micro&microµcro;30 µm-thick sections stained with cresyl violet (an analine dye that preferentially stains RNA and DNA). Over 800 cases are now available.

Phenotypes of Major Recombinant Inbred Strains

(by Nathan Copeland; updated Jan 17, 2002 by RW).


Mouse Clearinghouse: Recombinant Inbred, Congenic, Consomic, etc.(soon)

Sharing Mice: This clearinghouse is a simple way for you to find out who has different types of strains of mice. It is meant as a tool to encourage collaborative use of unique genetic resources. Please register your interest in particular lines. Please also enter a list of lines that may be available from your colony. By viewing other entries in this database you can find out about new strains that are being generated and that may soon be available. The clearinghouse is open to submissions from all groups with mouse stock, including those with recombinant inbred strains, congenic lines, chromosome substitution strains, or other mice that are difficult to obtain. You are welcome to register "Requests" and "Interests" into your record in the database. You will be given a password so that you can update or delete your own records. For suggestions, problems, or questions regarding the Mouse Clearinghouse please contact Arthur Centeno at arthurgc_2000@yahoo.com. The database is moderated by R. Williams.


Table of Mouse Strains @ the MBL

A table that allows navigation between brain slides from different strains in the Mouse Brain Library.

Brain Weights of Strains of Mice @ the MBL

Average brain weigths of more than 230 types of mice. The database can be searched and sorted. SD is the standard deviation. CV is the coefficient of variation. Body weights are the means for our samples. Note that sex has no effect on brain weight in the mouse. Age has a small and inconsistent positive effect.

Brain Weight Database for Individual Mice @ the MBL

Brain weight, body weight, sex, age, litter size and litter parity (when known) for a set of approximately 9674 mice of different types. The database can be searched and sorted. Brain weights (usually after fixation) include the medulla and paraflocculi. Unfixed brain weights are typically 15 mg heavier. The column labeled litter is the number of animals in the litter on the day of birth. The next column (Parity) provides an index of the mother's age and experience, where Parity = 1 refers to animals that were in her first litter. To find a single strain you may find it helpful to begin your entry with an equal sign, for example enter "=C57BL/6J" to get data for ~130 of these mice.


Strain Variation in Retinal Ganglion Cell Number

A summary of the main results of our analysis of the retinal ganglion cell population of over 573 mice belonging to 62 strains.


Individual Counts of Retinal Ganglion Cell Number

A database in tab-delimited text format on the retinal ganglion cell population size of approximately 573 mice belonging to more than 62 distinct strains. Use a spreadsheet program to view these data. All estimates have been reviewed and more than 146 cases have been replicated. This database is in progress and does contain some errors (536 KB).


Olfactory Bulb Weight Data

A small text-format tab-delimited database on olfactory bulb weight for a set of approximately 400 mice used to map four bulb-specific QTLs. Import data from this file into a spreadsheet program to view these data. This file accompanies a paper in Behavior Genetics by Williams and colleagues (2000).


Animal Colony Databases

MouSeek: A FileMaker Pro Colony Database

by Caleb F. Davis
Jeff Noebels laboratory, Baylor College of Medicine

MouSeek is a set of eight related databases can be used to keep track of any mouse colony. The databases can be easily modified to fit most rodent colony applications. Even if you have limited experience with databases, you will find FileMaker and MouSeek user-friendly enough to make the transition to a colony database painless. For details on MouSeek see the help file.

For details and commentary on MouSeek subscribe to the MouSeek LISTSERV at www.egroups.com/group/mouseek

The entire set of MouSeek data files can be installed by downloading MouSeek.sit or MouSeek.zip to a single directory using a third party utility (StuffIt or WinZip). If you want to test these files but do not have FileMaker Pro, you can download a free test version at http://www.filemaker.com and then double-click on the file named Options.fp3 to run the program.

The two links below are compressed versions of MouSeek. Expand one of the archives and put its files in a single folder.


These are the individual files that make up MouSeek:

  1. Options.FP3
  2. MiceEdits.FP3
  3. Cages.FP3
  4. Mice.FP3
  5. LitterEdits.FP3
  6. Litters.FP3
  7. Transactions.FP3
  8. Breeders.FP3




Williams Lab FileMaker Pro Colony Databases

The following four databases (which require FileMaker Pro version 3, 4, 5 or 5.5 respectively) are used by R. Williams and colleagues. They can be used to assemble an inexpensive but powerful relational database to help maintain a mouse colony. Download all four files. Each file include some of our mouse colony data so that you can see relationships among files. If you decide to use the databases, simply delete of our data. If you want to test these files but do not have FileMaker Pro, you can download a free test version at http://www.filemaker.com.

  1. LitterDB.fp3 | LitterDB.fp5.5
    One of the set of four related databases used to manage a mouse colony. New litters are entered in this database. Note: many of the sorting buttons along the top of forms need to be activated by attaching simple scripts. Read through the FileMaker Pro manual to learn how to do this. The process is simple. When you open these files they may ask you to link to related files that you do not have (e.g., PerfusionDB). To eliminate this request simply delete the relationship (see "Relationships..." under the File menu heading).

  2. CageDB.fp3 | CageDB.fp5.5
    The cage database is used to track the history of a particular mouse cage. This database is similar in use to the cage cards attached to each cage in a colony.

  3. CageLocationDB.fp3
    This database tracks the position of a cage in a rack and room. Used to track total mouse use.

  4. BreederDB.fp3 | BreederDB.fp5.5
    A database used to follow the history of mice used for breeding.




Truett Lab FileMaker Pro Colony Databases


  1. Mice.fp3
    The first of two FileMaker Pro colony databases by Gary Truett used to follow the history of mice used for breeding. This database contains the records for all mice. For other details on using this file see Gary's comments about using these files.

  2. MiceDams.fp3
    The second of two FileMaker Pro colony databases by Gary Truett used to follow the history of mice used for breeding. This database contains breeding records of individual dams. See Gary's comments about using these files.


Information and Other Projects


Gene Map Data Repository at UT Memphis

A repository of information useful for mapping genes or QTLs. Data on our neurogenic QTLs will be made available in Map Manager format. The Map Manager QT files will be useful only if you have already downloaded Map Manager QT from Ken Manly. You can obtain Map Manager via FTP from Roswell Park Cancer Institute.


Since 11 August 98. Updated Jul 30, 2002


Short Course Tutorial
Neuroscience Meets Quantitative Genetics: Using Morphometric Data to Map Genes that Modulate CNS Architecture
Updated August 2000 with new figures and text on RIX mapping.

  Learn More

More Publications
Related Sites

Neurogenetics at University of Tennessee Health Science Center

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Robert W. Williams | Alex Williams 2002, Nervenet.org