UNC Systems Genetics Core

The SGCF is able to provide mice to both internal and external customers. Shipping couriers are able to transport mice to most locations, but please note that some shipping delays or cancellations may occur without notice.

Please continue to contact either the Core Director, Rachel Lynch or Darla Miller at sgcf@unc.edu for questions regarding new or existing orders. 


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

The strains of the CC at least 90% homozygous are available to other researchers to use.  These strains are 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 is below.

UNC Systems Genetics Core Mice, Products & Services Conditions of Use

"MICE" means mouse strains, their progeny derived by inbreeding or crossbreeding, unmodified derivatives from mouse strains or their progeny supplied by UNC Systems Genetics Core. "PRODUCTS" means biological materials supplied by UNC Systems Genetics Core, and their derivatives. "RECIPIENT" means each recipient of MICE, PRODUCTS, or services provided by UNC Systems Genetics Core including each institution, its employees and other researchers under its control. MICE or PRODUCTS shall not be: (i) used for any purpose other than the internal research, (ii) sold or otherwise provided to any third party for any use, or (iii) provided to any agent or other third party to provide breeding or other services. Acceptance of MICE or PRODUCTS from UNC Systems Genetics Core shall be deemed as agreement by RECIPIENT to these conditions, and departure from these conditions requires UNC Systems Genetics Core's prior written authorization.

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.  

 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.  


FOR GENOTYPING, please contact Transnetyx (https://www.transnetyx.com/)

Mouse Universal Genotyping Array (MUGA and GigaMUGA)

MUGA: Approximately 10,000 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/HlLtJ [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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