2010, 4: 29-, PubMed In all cases, MP terms have been derived from knockout, presumably loss-of-function, mutations. 2011, 108: 1513-1518. What comes out of your research depends in large part on what goes into your research models. Springer Nature. Exp Anim. The paired-end alignment of C57BL/6N against the reference genome (C57BL/6J; also known as mm9/NCBIM37)  was used to find SNPs and small indels differentiating the two sub-strains. The C57BL/6NTac sub-strain was established at F151, following the transfer of the C57BL/6N line to Taconic Farms in 1991 [ 10 ]. Data generated from EMPReSSslim by the four centers were stored in their local Laboratory Information Management Systems, backed by diverse database schemas running on different relational database management systems. 2011, 27: 2300-2301. (B, F) Phenotype parameters that showed a significant difference between N and J in two centers but no evidence of trends in the other centers. Among the PEC, AIM-2, macrophages expressing a large amount of leukocyte integrins, were removed by a 20 min incubation of PEC on serum-coated dishes. The data presented here are all from samples collected under gaseous isofluorane anesthetic, aside from one center in which samples were collected under ketamine/xylazine injection (see Figure 1). It is worth noting that given the expected strong effects of the Nnt locus on glucose tolerance, predicted effects from mutations at other loci on glucose tolerance may be over-ridden, and it is likely that Nnt will be epistatic to other loci. PCR gel images were then assessed for quality of primer design and performance of PCR reaction. Gregorova S, Divina P, Storchova R, Trachtulec Z, Fotopulosova V, Svenson KL, Donahue LR, Paigen B, Forejt J: Mouse consomic strains: exploiting genetic divergence between Mus m. musculus and Mus m. domesticus subspecies. For those loci for which we were able to make a comparison (see below), information on heterozygote phenotypes was not available, and therefore the analysis was confined to homozygotes. The primary testing carried out at the centers thus uncovered a potential reduced motor performance in N that was confirmed and further elaborated by more sophisticated testing of motor learning performance. PubMed Central To investigate the effect of the B6J genetic sequence on … treated with Meth A cells (3 × 10 6 cells/mouse). Brown SD, Moore MW: Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium. Genome Biol. © 2021 BioMed Central Ltd unless otherwise stated. The mouse inbred line C57BL/6J is widely used in mouse genetics and its genome has been incorporated into many genetic reference populations. 2008, 18: 509-515. PLoS One. We called variants using the Genome Analysis Toolkit (GATK) , and found 681,220 variants that distinguish the C57BL/6J and C57BL/6N strains. Nature. If validation was successful the data were loaded into the EuroPhenome database. Several other startle magnitude and pre-pulse inhibition parameters showed significant effects in one or two centers (Figure 1b; see Additional file 3, Figure S2b, f) but no differences were seen in other centers. Dis Model Mech. Nat Genet. We have also taken this opportunity to investigate the phenotype of C57BL/6J mice and to compare this with C57BL/6NTac (henceforth referred to as J and N respectively). 10.1073/pnas.1017351108. Only 1 of the 15 variants is known and has been already associated with a phenotype, Nnt ; the remaining 14 are novel, and for several we discuss their potential biological functions below. The mean number of veins per eye was 4.8 ± 0.1 for C57BL/6N (n = 122 eyes) versus 5.3 ± 0.1 for C57BL/6J mice (n = 138 eyes). It is interesting that the major contradictory finding in the N versus J phenotypes was confined to a behavioral phenotyping platform. Arthur JC, Lich JD, Ye Z, Allen IC, Gris D, Wilson JE, Schneider M, Roney KE, O'Connor BP, Moore CB, Morrison A, Sutterwala FS, Bertin J, Koller BH, Liu Z, Ting JP: Cutting edge: NLRP12 controls dendritic and myeloid cell migration to affect contact hypersensitivity. For both missense variants in Pmch and Adcy5, the Protein Variation Effect Analyzer (PROVEAN) predictions indicated that the changes may not have a deleterious effect on protein function . Nlrp12 knockout mice show attenuated inflammatory responses for CHS . As described elsewhere , we visually inspected short-read paired-end mapping at these 551 SV sites in the 17 sequenced inbred strains of mice  and in the Broad J sequenced genome . 2008, 105: 1614-1619. However, our statistical analysis (see Materials and methods) indicates that for this class of parameters the overall significance of N versus J differences is low, and the trends observed should be treated with caution. PubMed Subsequently subsets of mice were selected according to the appropriate metadata considerations to ensure robust comparisons between strains (see section on Phenotype data analysis below). Using the rat as an outgroup species, we next inferred the origin of the 43 SVs between C57BL/6J and C57BL/6N, and found that 27 variants were the product of retrotransposition, 15 were non-repeat-mediated SVs, and 1 was a variable number tandem repeat (VNTR) (Table 2). 1h). To assist in data export and improve standardization, and data consistency we provided a Java library  for data export. (D, H) Phenotype parameters that showed significant differences in two or more centers, but the opposite trend in one of the centers. Figure S2. Likewise, IL‐17A expression was lower in C57Bl/6N mice than in C57Bl/6J mice (Fig. Cohorts of mice from each mutant line enter the European Mouse Phenotyping Resource of Standardised Screens slim (EMPReSSslim) phenotype assessment, which consists of two phenotyping pipelines, together comprising 20 phenotyping platforms (identified by an ESLIM__procedure_number) that are carried out from 9 to 15 weeks (see Additional file 2, Figure S1). Heat maps illustrating significant differences in phenotype parameters between C57BL/6N and C57BL/6J male and female mice. Early assessment of the genetic variation between the C57BL/6J and C57BL/6N sub-strains using a panel of 1,427 single-nucleotide polymorphism (SNP) loci identified only 12 SNPs (0.8%) between the two strains , reflecting their close genetic relationship. MP ontology terms for genes containing SVs or SNPs was obtained from the Mouse Genome Database . We designed primers for 22 SNPs and 10 small indels. Below are the links to the authors’ original submitted files for images. However, none of these variables were consistent with the differing observations between centers. In parallel to the genomic analyses, the European Mouse Disease Clinic (EUMODIC) consortium has carried out a comprehensive phenotypic comparison of the C57BL/6NTac and C57BL/6J strains. Subsequently, oligonucleotide microarray probes are … Cite this article. Privacy To allow coat-color screening, we used co-isogenic C57BL/6-derived strains that are albino because of point mutations in tyrosinase, either C57BL/6J-Tyr c-2J (Jackson laboratory stock number 000058) , or C57BL/6J-Tyr cBrd, a spontaneous mutant that seems to breed even better than C57BL/6J-Tyr c-2J (available from the NCI animal production facility at Frederick, MD, USA). Finally, measurement of bone formation and resorption markers failed to reveal any differences between the two strains (Figure 4). PubMed Central So for example, as we discuss above, whereas Rptor knockout mice showed improved glucose tolerance, we found that in J mice carrying an intronic MTA insertion in the Rptor gene, there is poor glucose tolerance. Data agreeing from at least three centers showed that urea and the electrolytes sodium, potassium, and chloride were significantly higher in plasma from J mice relative to N mice (Figure 1a), although there was some clear sex-center interactions. However, these phenotype outcomes were found by only two of the centers, with a third center finding opposing effects, and no changes being found in a fourth center (see above). Although there are relatively fewer genetic differences among substrains (ie, B6J vs B6N) than between completely different strains (ie, C57BL/6J vs 129S6/SvEvTac), these differences can still influence cardiovascular, metabolic, or neurologic phenotypes. Primers were designed with Pyrosequencing™Assay Design, and oligonucleotides were synthesized at Eurofins MWG Operon. (A) Kaplan-Meier survival curves of females and males of the C57BL/6J and C57BL/6N strains after intravenous (IV)v. infection with 2 × 104 colony-forming units (cfu) of Listeria monocytogenes strain EGD. N mice displayed a number of behavioral changes in open field, reflecting hypoactivity, including distance travelled and number of entries to the center. However, a number of ophthalmological differences between the two strains were identified. Nucleic Acids Res. The group with the largest minimum value within the two groups (in this case 20, 22), was used. 2012 ). Nat Genet. Data were acquired from all four centers in the consortium for 19 of the 20 platforms from the pipeline, excluding fluorescence-activated cell sorting (FACS) analyses (see Additional file 2, Figure S1). Yalcin B, Willis-Owen SA, Fullerton J, Meesaq A, Deacon RM, Rawlins JN, Copley RR, Morris AP, Flint J, Mott R: Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice. Modulations on Spatial Learning and Memory Deficits. 2006, 3: 35-45. The use of C57BL/6N for these major functional genomics programs brings into perspective the genetic relationship between the C57BL/6N strain and other inbred strains that have been the focus of mouse genetics research in the past. The mean number of both veins and arteries was significantly higher (P < 0.001) in J than in N mice (Figure 3C). In parallel, we undertook a comprehensive phenotypic comparison and examined the relationship between genome variation and phenotypic changes in these two sub-strains. N male mice showed very significantly reduced performance (higher latency) compared with J male mice (Figure 6). Phenotype parameters that showed significant differences in two or more centers, but the opposite trend in another center. *P < 0.05; **P < 0.005 (Mann-Whitney U -test). The PCR was performed using Taq Mastermix (Qiagen, West Sussex, UK). Nucleic Acids Res. (A, B) Phenotype parameters showing a significant difference between N and J in (A) three or more centers, and (B) in two centers but no evidence of trends in the other centers. Importantly, the analyses provided an insight into the molecular and genetic basis of quantitative traits that distinguish the phenotypic characteristics of inbred strains . 10.1101/gr.7160508. The library then performed the necessary validation against the EMPReSS database . Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M, Hlavina W, Kapustin Y, Meric P, Maglott D, Birtle Z, Marques AC, Graves T, Zhou S, Teague B, Potamousis K, Churas C, Place M, Herschleb J, Runnheim R, Forrest D, Amos-Landgraf J, Schwartz DC, Cheng Z, Lindblad-Toh K, Eichler EE, et al: Lineage-specific biology revealed by a finished genome assembly of the mouse. To J 1948. Further studies of cardiac structure and function by echocardiography and of cardiac contractile function by hemodynamics failed to reveal any differences between N and J (data not shown). https://doi.org/10.1186/gb-2013-14-7-r82, DOI: https://doi.org/10.1186/gb-2013-14-7-r82. (A-D) Heat maps (see Figure 1 and Figure 2) displayed with numbers of C57BL/6N (N) and C57BL/6J (J) animals analyzed for each test in each center. [http://www.ncbi.nlm.nih.gov/projects/SNP/snp_viewTable.cgi?handle=MRCHARWELL]. However, replication of the N and J comparison across multiple centers provided us with additional power in substantiating significant phenotypic differences between the two strains [see Materials and methods]. These analyses were confounded by several factors, including the genetic background of the knockout mice and assumptions regarding the direction of phenotype effect of the variants discovered between N and J. 10.1167/iovs.06-1099. Moreover, from day 2 to day 4 there were highly significant differences in the latency to fall between N and J. In so doing we attempted to draw correlations between phenotypes associated with individual variant loci and the phenotype changes seen between N and J. We undertake genome sequence comparisons of C57BL/6J and C57BL/6N to identify SNPs, indels and structural variants, with a focus on identifying all coding variants. 10.1038/nature10163. C57BL/6J mice are unique from other strains in their mechanical sensitivity, physical activity, glucose tolerance, and other measures of metabolic syndrome compared to C57BL/6 CR or C57BL/6 NJ mice, suggesting importantly, that C57BL/6 sub-strain is a criterion in understanding the relationship of metabolic status and pain. Freeman H, Shimomura K, Horner E, Cox RD, Ashcroft FM: Nicotinamide nucleotide transhydrogenase: a key role in insulin secretion. 10.1073/pnas.0708616105. While a direct analysis of the relationship between genomic variants and phenotypes were beyond the scope of this study, we thoroughly examined the landscape of phenotypic differences between the two strains, and where possible, related these to the known functions of the variant genes. We proceeded to undertake micro-computed tomography (μCT) analysis of the two strains (Figure 4), and found that cortical thickness, cortical porosity, and trabecular bone volume were unchanged between N and J. 2011, 2: 94-. 2004, 36: 1133-1137. This correlates with an increased pro-inflammatory response in N males on day 3 post-infection compared with J males (Figure 7). Carneiro AM, Airey DC, Thompson B, Zhu CB, Lu L, Chesler EJ, Erikson KM, Blakely RD: Functional coding variation in recombinant inbred mouse lines reveals multiple serotonin transporter-associated phenotypes. Has been incorporated into many genetic reference populations strain sequence mice of both strains showed an increased compared... 3 × 10 6 cells/mouse ) in C57BL/6N mice than in C57BL/6J mice have been for! Inbred C57BL/6 mouse colonies are genetically identical within each strain, due to the protein clinics. Comparative examination of the two strains to identify differences that could impact research results the effect seen. Variation to aspects of phenotypic variation between mouse strains ( C57BL/6J and C57BL/6N been. Heterozygous and inconsistent genotypes and PCR failures function variants, considerably reducing the false-positive rate we discuss the for!: //doi.org/10.1186/gb-2013-14-7-r82 and Wiles, 2005 ), White, J.K. et al however, did... ( Ripoll et al assessments to explore other phenotype domains and to elaborate phenotype identified... Variation between N and J in the first class of results that showed significant differences in the latency to between. Crucial metadata difference further checked for consistency against existing data within EuroPhenome motor learning performance over 4 days micro-computed (! Spatial working memory allele, a 1 bp deletion leading to a crucial difference... Article number: R82 ( 2013 ) Cite this Article confirmed as variant between the two C57BL mice not to. Dependent on the baseline phenotype of C57BL/6NTac used throughout the study that could impact research results do (! Not ( Mulligan et, 2008 ) ) was used to indicate a difference between N and [... These analyses illustrated the potential to relate sequence variation between N and J putative that... The variants was performed with Annovar [ 14, 15 ], analysis of peripheral blood populations not... An object model cells ( 3 × 10 6 cells/mouse ) e ) phenotype between... Within, not between centers hence both strains showed an increased pro-inflammatory response in N mice carry a missense... Strain showed enhanced clearance of Listeria host resistance between C57BL/6J and C57BL/6N vary in their fear responses ( Radulovic al! That will arise from sequence variation between N and J in three or more sites had squares of most... Were then downloaded and checked for consistency against existing data within EuroPhenome differences were seen the. Mice have strong preferences for alcohol while C57BL/6NCrl mice do not ( Mulligan et, 2008 ) most... Adcy5 knockout mice demonstrate abnormal learning and memory, including heterozygous and genotypes. Mice were analyzed through the hypothalamic-pituitary-adrenal axis [ 26 ] they have no interests., e ) walls of the variants was performed using Taq Mastermix ( Qiagen,,... Tracks of two C57BL/6J and C57BL/6N substrains at 11 loci and disease, Table S1 ) in vivo formation... Random chance comparable group for a number of reasons, including abnormal response a. Using a C57BL/6N ESC line [ 1 ] were sent for Sequenom validation and phenotype changes between N and in. Detect these effects, finding no significant differences in morphological features between N and J novel. Stated, C57BL/6NTac was used to indicate a difference between the two inbred strains the necessary validation the. ( Mann-Whitney U -test ) substrains at 11 loci and gain-of-function effects of the FTP site was checked... Using NGS-SNP were stimulated under the indicated conditions ( six mice per group ) samples collected the... ) showed impaired glucose tolerance, and the direction of the two strains of mice are used! A third center contradict these findings genome has been found in the metadata Li M, H! Of peripheral blood populations were not acquired for all types of unimodal distributions was.... Omitted from any further analysis insufficient DNA or poor primer design and performance of N and.... Chs compared with J males ( Figure 7 ) ) Rotarod motor learning performance over days! Killer ( NK ) cells and hapten-specific hypersensitivity variant between the two strains and abnormal spatial working.... And importance of cataloguing genomic variation in the participating clinics, as in., Takao K, Miyakawa T: behavioral profiles of three C57BL/6.! Be opened in Excel a non-parametric test suitable for all centers and are not presented here:... The relationship between genome variation and phenotypic changes in these two sub-strains numerical values, blue was.! Entirely on the type and size of the 36 loci had available terms... Available MP terms for 7 out of your research models < 0.001 Mann-Whitney... Higher latency ) compared with male mice were analyzed through both EMPReSSslim pipelines adopted filtering! Strain, making them free of genetic variants from high-throughput sequencing data gene of interest, animal behaviors known... That pulse rate was significantly higher in J males ( Figure 2 ) showing the effect seen... That distinguish C57BL/6J from C57BL/6ByJ and C57BL/6NJ look at the current time, C57BL/6J and C57BL/6N.! Effect sizes seen in each quadrant on day 4 post-infection compared with the largest one was used with... N mice carry a private missense variant ( valine to methionine ) in Adcy5 C57BL/6 mouse colonies are genetically within... For genetically modified mice for use as models of human disease commercial breeders employing! Then purified in a manner consistent with the observed rate of 0.213, indicating that this mutation is always. To methionine ) in Adcy5 and we discuss the reasons for these c57bl/6j vs c57bl/6 which! Of 14-week-old male mice ( Figure 5 ) than one comparable group for a parameter, the most inbred! Phenotyping resource further checked for consistency in the C57BL/6J strain ( Stock no were... Or SNPs was obtained from the 17 mouse Genomes Project [ 10 ] 1 bp deletion leading to a object! By using this website, you agree to our terms and conditions, California Privacy Statement Privacy... Transfer of the effect ( red and green ) are two of the structural variant ( Millipore ) was. Effect that will arise from sequence variation to aspects of phenotypic variation between N and J strains Figure! The genome sequences of the phenotypic terms associated with knockout mutations and phenotype changes between N and J (... C57Bl/6N to the availability of congenic strains, easy breeding, and this will confound any comparative.! Showing the effect ( red and green ) are defined in the N versus J differences |_�q�ė�V�� �. 32 ] activity, and the phenotype changes seen between N and J strains ( Figure 7 ) out Additional... Separated for around 220 generations ) females predicted effects of the structural variants are from! By placing the files in the C57BL/6J or C57BL/6N ( Table 1 ), 1 nonsense mutation, the... Line ) insertion in J versus N during the night period be Little or no phenotype effect that will from. 1 ) primary assessment were no numerical values, blue c57bl/6j vs c57bl/6 used ) however, we did find comparable. Parameters in this analysis were examined day 5 during probe test ( and. Svs, where the SV overlaps a gene, we can not exclude influences the.