UNC Systems Genetics Core


What is the Systems Genetics Core at UNC?

The Systems Genetics Core at UNC was established to provide Collaborative Cross mice and genotypes to investigators both at UNC Chapel Hill and at other institutions.

What is available from the Systems Genetic Core at UNC?


Collaborative Cross mice

Once the lines of the CC become at least 90% homozygous, they will be made available to other researchers to use.  These strains of mice will be available to any investigator at any institution for internal use.  However, the CC mice come with conditions of use such that they cannot be bred for and/or redistributed without prior consent from the originators of the CC line.  The COU and ordering can be found under the "Ordering" tab. 

To see the available CC RI lines please see "Available Lines"

Special Orders

Recombinant Inbred Crosses (RIX)

The CC lines can be crossed to make F1s.  We can set up crosses of your choice and progeny of those crosses either tested, dissected or shipped to you.  Please contact Darla Miller at millerdr@med.unc.edu for more details.

 Recombinant Inbred Backcrosses (RIB)

Specific Crosses to a model of your choice can be done in our facility and the progeny either tested, dissected or shipped to you.  Please contact Darla Miller at millerdr@med.unc.edu for more details.


Mouse Universal Genotyping Array (MUGA and GigaMUGA)

MUGA: Approximately 7500 SNP array specifically designed to identify the founder strains of the CC, but useful for almost all strains of mice. 

MUGA is a 7851-SNP marker genotyping array built on the Illumina Infinium platform. SNP markers are distributed throughout the mouse genome with an average spacing of 325 kb (SD 191 kb). The markers were chosen to be maximally informative and maximally independent for the eight founder strains of the CC. This combination was achieved by selecting SNPs with high minor-allele frequencies (maximizing entropy) and low local pairwise linkage disequilibrium (minimizing mutual information). The design criteria make the platform optimal for detecting heterozygous regions, while in homozygous regions they allow for optimal discrimination between haplotypes. These optimization criteria are population dependent.

GigaMUGA: A third generation array called GigaMUGA consisting of approximately 150,000 SNPs is currently available.

Retired arrays: Mouse Universal Genotyping Array (MegaMUGA)

The panel consisting of 77,000 SNPs called MegaMUGA is no longer available.

Mouse Diversity Array (MDA)

A high density array of approximately 550,000 SNPs on the platform is also no longer available.

CC Strain Colors


CC Designation Strain Jax Catalog No Web Color rgb Color
A A/J [1] 000646 #ff0 240,240,0
B C57BL/6J [2] 000664 #888 128,128,128
C 129S1/SvImJ [3] 002448 #f88 240,128,128
D NOD/ShiLtJ [4] 001976 #11f 16,16,240
E NZO/H1LtJ [5] 002105 #0cf 0,160,240
F CAST/EiJ [6] 000928 #0a0 0,160,0
G PWK/PhJ [7] 003715 #f00 240,0,0
H WSB/EiJ 001145 #90e 144,0,224

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