UNC Systems Genetics

CC Periodic Table

In any publication, please refer to the CC animals by their full CCxxx/nnnn nomenclature.

 In any publication, please acknowledge the origin of the CC mice used as follows:

For CC strains with the laboratory code “Tau”: Tel Aviv University, Israel1
For CC strains with the laboratory code “Geni”: Geniad, Australia2
For CC strains with the laboratory code “Unc”: University of North Carolina, US4
The following paragraph is provided as an example on how to cite the provenance of CC mice used in your study
Mice were obtained from the Systems Genetics Core Facility at the University of North Carolina3.  Previous to their relocation to UNC, CC lines were generated and bred at Tel Aviv University in Israel1, Geniad in Australia2 and Oak Ridge National Laboratory in the US4.
1. Iraqi, F. A., G. Churchill, and R. Mott, 2008 The Collaborative Cross, developing a resource for mammalian systems genetics: A status report of the Wellcome Trust cohort. Mamm. Genome 19: 379–381.
2. Morahan, G., L. Balmer, D. Monley 2008 Establishment of "The Gene Mine": a resource for rapid identification of complex trait genes. Mamm. Genome 19:390-393.
3. Welsh CE, Miller DR, Manly KF, Wang J, McMillan L, Morahan G, Mott R, Iraqi FA, Threadgill DW, Pardo-Manuel de Villena, F. (2012). Status and access to the Collaborative Cross population. Mammalian Genome. 23:322-35. PMID22847377. PMC3463789.
4. Chesler, E. J., D. R. Miller, L. R. Branstetter, L. D. Galloway, B. L. Jackson, et al., 2008 The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics. Mamm. Genome 19: 382–389.


Download all mice haplotype data in one zip file here and all the data from the table below here.


The strains listed on this page are the CC strains that have reached the following criteria: 1) are approximately at least 90% homozygous, 2) have 6 to 8 founders, 3) are in SPF or barrier status, 4) will be available from UNC. Some strains are harder to breed than others, so availability may vary.  The UNC Systems Genetics Core Facility can provide breeding stock (for internal use unless other permission is acquired) or experimental cohorts. We have attempted to include as much breeding advice as possible, but feel free to contact Darla Miller if more advice is desired.

Our goal to give access to all investigators to the CC resource.  We have shown that even incipient inbred lines are a powerful genetic resource.  Distributing strains that are not 100% inbred addresses the fact that some strains become increasingly difficult to maintain with terminal inbreeding and thus may be lost.  Researchers need to carefully evaluate whether the CC strains meet the needs of their experimental design.  However, we wish to note that for decades geneticists have used resources with similar shortcomings and that in contrast with these historical resources, users of CC strains will know, with an unprecedented level of detail, which regions are not fixed and what alleles are segregating in these regions.

Those regions that are still segregating, as well as fixed genomic regions, are documented and accessible from this web site. They can be examined by choosing any strain, proceeding to the "More Info" section, and then clicking on the strain's name. The most recent genotypes can also be downloaded from the "More Info" page (many of these genotypes are at least four years old, so the animals you receive will almost certainly be more inbred than these genotypes demonstrate.). Note: these are likely to differ from the genotypes supplied on the "Information" page, as those genotypes were snapshots of the genome of a single male sample from each line, which are now separated by ten or more generations from the distributable strains.


Strain Name is the designation for an available strain. Each name indicates one of the three original breeding populations and a strain number. All listed strains are currently finishing inbreeding at UNC-Chapel Hill.

    OR = The lines started at the Oak Ridge National Laboratory and moved to UNC-Chapel Hill.
    IL = The lines started in Kenya and moved to Tel Aviv University, Israel.
    AU = The lines started by Geniad in Western Australia.

    Completed strains will come from all three populations. They will use the CC designation and be assigned sequential strain numbers along with a standard laboratory designation (ex. CC001/Unc, CC002/Tau, etc.). For a limited time period, we will track, via an "alternative name", the names of distributable lines that are related to a completed strain.

% Het

    An upper bound on the maximum residual heterozygosity of the strain as determined by the joint heterozygosity of obligate ancestors.

Health Status

    '1' = ultra clean barrier facility*, '2' = SPF facility**

More Info

    Genome annotations (fixed and segregating regions), latest genotypes, breeding data, coat colors, etc. are available. 

Standard housing/breeding of the CC
Cages:    All cages are Autoclaved
               Tecniplast Greenline Ventilated Cages are used for pair or trio matings                                     

Autoclaved and Irradiated ¼″ Bed-o’Cobs by The Andersons Lab Bedding Products (https://andersonslabbedding.com/wp-content/uploads/2012/07/Bed-oCobs_1_4.pdf)
ALPHA-dri® from Shepherd Specialty Papers (http://www.ssponline.com/alpha_dri.htm)

Enrichment:   Nestlets, sterile Sunflower seed enrichment (~1-2Tbs. added to bottom of cage approx. 1x/week for foraging) for breeders unless otherwise noted (https://www.bio-serv.com/product/SFS.html)

Water:          Auto water 

Feed:           LabDiet® Select Verified Rodent Diets 5V0F - Select Rodent 50 IF/6F Auto (https://www.labdiet.com/cs/groups/lolweb/@labdiet/documents/web_content/ndjf/oda0/~edisp/36142_804403.pdf)

Breeder Chow – autoclaved Harlan 2019SX is now LabDiet® Select Verified Rodent Diets 5V0G - Select Rodent 50 IF/9F Auto (https://www.labdiet.com/cs/groups/lolweb/@labdiet/documents/web_content/ndjf/odq5/~edisp/36142_849601.pdf)


Column Headings Key:

  • days det Het =  days since determination of Heterozygosity
  • sex ratio =  sex ratio at weaning
  • %M prod litters =  fraction of males that produce litters
  • F prod fertile M =  fraction of females that produce litters with known fertile males
  • breed well w/F =  breed well in multiple-female cages


* designated health status '1' negative for all of the following: by serology - MHV, MVM, NS1, MPV(MPV1, 2, 3), MNV, TMEV, EDIM, Sendai, and Mycoplasma pulmonis. Additionally, some are tested for PVM, Reovirus 3, LCM, Ectromelia, MAD1, MAD2 and Polyoma, by culture nasal swab - Pasteurella pneumotropica, by fecal PCR - Helicobacter

** designated health status '2' negative for all of the following: by serology - EDIM, TMEV GDVII, MHV, Mycoplasma pulmonis, MPV, MVM, Parvo NS-1, PVM, and Sendai. Additionally, some are tested for CAR bacillus, Ectromelia, LCMV, MAD1, MAD2, mCMV, Polyoma, and REO3.

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