UNC Systems Genetics Core


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.

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.

Tier 1 CC Strains
Strain Name Alias Alt. Name # Founders % Het Status More Info
CC001/Unc OR13140 8 4.6 1=Barrier
CC002/Unc OR15156 8 10.2 1=Barrier
CC003/Unc OR13067 8 8.9 1=Barrier
CC004/TauUnc IL16188 IL188A 8 5.2 1=Barrier
CC005/TauUnc IL16211 IL211A 8 1.1 1=Barrier
CC006/TauUnc IL16750 IL2750 8 8.3 1=Barrier
CC007/Unc OR13421 8 9.8 1=Barrier
CC008/GeniUnc AU8036 BOON_HF 8 5.3 2=SPF
CC009/Unc OR5489 8 8.4 2=SPF
CC010/GeniUnc AU8018 NUK_AC 8 3.4 1=Barrier
CC011/Unc OR3252 8 5.9 2=SPF
CC012/GeniUnc AU8005 DAVIS_BA 8 9.3 2=SPF

Other Available CC Strains
Strain Name Alias Alt. Name # Founders % Het Status More Info
CC013/GeniUnc AU8010 GIG_EF 7 0.5 2=SPF
CC015/Unc OR3154 8 8.6 2=SPF
CC016/GeniUnc AU8024 SAT_GA 7 3.7 2=SPF
CC017/Unc OR3032 8 7.4 2=SPF
CC018/Unc OR3609 8 9.6 2=SPF
CC019/TauUnc IL16513 IL2513 6 9.0 1=Barrier
CC020/GeniUnc AU8054 JUNIOR_GB 8 4.5 2=SPF
CC021/Unc OR1566 8 6.3 2=SPF
CC022/GeniUnc AU8046 MEE_AG 8 7.4 2=SPF
CC023/GeniUnc AU8043 TOP_DA 8 8.6 2=SPF
CC024/GeniUnc AU8004 CIS_AD 8 3.6 2=SPF
CC025/GeniUnc AU8008 FEW_FD 8 5.3 2=SPF
CC026/GeniUnc AU8026 TAS_FE 7 4.6 2=SPF
CC027/GeniUnc AU8027 TOFU_FB 8 8.2 2=SPF
CC028/GeniUnc AU8016 JUD_EF 8 2.1 2=SPF
CC029/Unc OR3564 8 8.9 2=SPF
CC030/GeniUnc AU8034 ZIF2_FC 8 8.4 2=SPF
CC031/GeniUnc AU8031 WAB2_DH 6 8.3 2=SPF
CC032/GeniUnc AU8002 BEM_AG 7 8.6 2=SPF
CC033/GeniUnc AU8033 YID_FH 8 9.3 2=SPF
CC034/Unc OR5080 8 9.3 2=SPF
CC035/Unc OR5035 8 11.2 2=SPF
CC036/Unc OR477 8 9.0 2=SPF
CC037/TauUnc IL16072 IL72 6 1.1 1=Barrier
CC038/GeniUnc AU8049 ROGAN 8 4.3 2=SPF
CC039/Unc OR15155 8 10.3 1=Barrier
CC040/TauUnc IL16557 IL57 8 11.4 1=Barrier
CC041/TauUnc IL16441 IL4141 6 9.5 1=Barrier
CC042/GeniUnc AU18042 BOM_GB 7 6.3 1=Barrier
CC043/GeniUnc AU8021 PIPING_BD 8 4.7 2=SPF
CC044/Unc OR4410 8 10.2 2=SPF
CC045/GeniUnc AU8045 DAM_HG 8 11.7 2=SPF
CC046/Unc OR5346 8 10.3 2=SPF
CC047/Unc OR5612 8 6.1 2=SPF
CC048/Unc OR5248 8 6.7 2=SPF
CC049/TauUnc IL16296 IL2296 8 13.1 1=Barrier
CC050/Unc OR867 8 4.6 2=SPF
CC051/TauUnc IL16912 IL1912 6 6.9 1=Barrier
CC052/GeniUnc AU8052 FUF_HE 8 10.4 2=SPF
CC053/Unc OR773 8 11.4 2=SPF
CC054/GeniUnc AU8050 CIV2_FE 8 10.5 2=SPF
CC055/TauUnc IL16680 IL2680 8 10.6 1=Barrier
CC056/GeniUnc AU8056 PUB_CD 6 4.3 2=SPF
CC057/Unc OR3393 8 10.7 2=SPF
CC058/Unc OR5358 8 15.0 2=SPF
CC059/TauUnc IL16012 IL3912 6 10.3 1=Barrier
CC060/Unc OR3460 8 14.6 2=SPF
CC061/GeniUnc AU8048 FIM_DF 8 5.1 2=SPF
CC062/Unc OR5306 8 11.8 2=SPF
CC063/Unc OR5391 8 7.2 2=SPF
CC065/Unc OR5119 8 8.1 1=Barrier
CC068/TauUnc IL16768 IL2668 8 14.1 1=Barrier
CC070/TauUnc IL16034 IL34 8 12.4 1=Barrier
CC071/TauUnc IL16785 IL285 8 12.8 1=Barrier
CC072/TauUnc IL16521 IL21 6 0.8 1=Barrier
CC073/Unc OR1515 8 6.6 2=SPF
CC074/Unc OR3015 8 10.3 2=SPF
CC075/Unc OR3260 8 11.9 2=SPF
CC076/Unc OR5343 8 12.9 2=SPF
CC078/TauUnc IL6126 IL2126 >10% 2=SPF
CC079/TauUnc IL6411 IL2011 >10% 2=SPF
CC080/TauUnc IL6573 IL2573 >10% 2=SPF
CC081/Unc OR3269 >10% 2=SPF

Download All Image, Haplotype, probabilities, and Genotype Files
Download All Distributable Lines Obligate Ancestor Information


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                                     
               Mouse cage-Sterile Multipurpose IVC are used for multi-female matings (We breed up to four females with one male.)
Bedding:     Autoclaved and Irradiated ¼ inch corn cob bedding
                  Diamond Dri  ¼ inch (soft white fluffy ) from Harlan Teklad
Enrichment:  Hard red shacks and nestlets
Water:         Autoclaved RO water
Feed:          Labdiet     Regular Chow– autoclaved Harlan 2020SX
                                  Breeder Chow- autoclaved Harlan 2019SX

* 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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