We present this powerful resource to the diabetes research community.
The Genomic study of parental mice database allows you to search gene expression in 6 key tissues (islet, liver, adipose, hypothalamus, gastrocnemius and soleus) as a function of genetic obesity (lean vs. OB/OB), strain (B6 vs. BTBR), and age (4 vs. 10 weeks), in our mouse model of Type 2 diabetes. You can search single genes, a list of genes or genes associated with a particular pathway and quickly view expression patterns across all groups in all tissues. You can perform correlations among genes, download the correlated gene list and perform ontology enrichment analyses.
The Genetic study of F2 cohort database derives from the construction of ~500 B6:BTBR F2 mice that were all sacrificed at the same age (10 weeks) and were all obese, thereby focusing the study on genetic differences between the parental strains. All F2 mice were genotyped at >2,000 informative SNPs, allowing us to link genotypic variation to phenotypic variation. Gene expression was profiled in 6 tissues (islet, liver, adipose, hypothalamus, gastrocnemius and kidney) in every F2 mouse. In addition, >100 diabetes-related clinical phenotypes were measured in all mice (e.g., plasma insulin). Tools are provided to determine genetic linkage for expression or clinical traits; eQTL and cQTL. Correlation analysis among genes or between genes and clinical phenotypes is also available.
The Collaborative Cross (CC) is a newly created panel of inbred mice that derives from 8 founder strains, including five classical lab strains (129S1/SvImJ, A/J, C57BL/6J, NOD/ShiLtJ, NZO/HILtJ) and three wild-derived strains (CAST/EiJ, PWK/PhJ and WSB/EiJ). The wild-derived strains contribute ~75% of the genetic diversity to the CC panel. The eight founder genomes are fully sequenced, providing a catalog of genomic variants that includes ~38M SNPs, ~ 5M small indels, and ~230K structural variants. Among annotated exons and UTRs of protein coding genes, there are SNPs in 94% of genes, indels in 66%, and structural variants in 12%. Effectively, every biological function of the organism is affected by genetic variation contained within the CC. We used these founder strains to study the relationship between genetic variation and gene regulation in pancreatic islets and liver, as well as metabolite variation in liver, plasma and gastrocnemius muscle. The CC founder characterization database provides a user-friendly web interface to search this unique resource.