Project description:The transcriptional profiles of ovarian tissue from four laboratory mouse-inbred strains were obtained with NIA15K-cDNA microarrays and then correlated with the divergent spontaneous ovarian tumor rates and reproductive parameters reported for each strain.
Project description:Gene-profiling of Tregs across inbred strains. There is a wide inter-individual range in the frequency of FoxP3+ Treg cells, but little is known about the underlying genetic or epigenetic mechanisms. We explored this issue accross inbred strains of mice. During this study, we established the gene expression profiles of Treg cells from the various inbred strains of mice.
Project description:We aimed to identify gene expression profiles/differences between spontaneously hypertensive rat(SHR) and normotensive rat (BN) in a set of recombinant inbred (RI) strains.
Project description:We aimed to identify gene expression profiles/differences between spontaneously hypertensive rat(SHR) and normotensive rat (BN) in a set of recombinant inbred (RI) strains.
Project description:BXH/HXB rat recombinant inbred (RI) strains are derived from the spontaneously hypertensive rat (SHR/Ola) and the Brown Norway congenic strains carrying the polydactylyl-luxate mutation (BN-Lx). Tissue from the apex of left ventricle of the heart was disected from 128 RI SHR/Ola and BN-Lx parental strains, RNA was extracted and labelled and hybridised to Affymetrix Rat Genome 230 2.0 Arrays.
Project description:We aimed to identify gene expression profiles/differences between spontaneously hypertensive rat(SHR) and normotensive rat (BN) in a set of recombinant inbred (RI) strains.
Project description:It is well established that epigenetic features, such as histone modifications and DNA methylation, are associated with gene expression across cell types. However, it is not well known how variation in genotype affects epigenetic state, or to what extent such variation contributes to variation in gene expression across genetically distinct individuals. Here we investigated the relationship between heritable epigenetic variation and gene expression in hepatocytes across nine inbred mouse strains. Eight of the inbred strains were founders of the diversity outbred (DO) mice, and the ninth was DBA/2J, which, along with C57BL/6J, is one of the founders of the BxD recombinant inbred panel of mice. We surveyed four histone modifications, H3K4me1, H3K4me3, H3K27me3 and H3K27ac, as well as DNA methylation. We used ChromHMM to identify 14 chromatin states representing distinct combinations of the four measured histone modifications. We found that variation in chromatin state mirrored genetic variation across the inbred strains. Furthermore, epigenetic variation was correlated with gene expression across strains. The correspondence between epigenetic state and gene expression was replicated in an independent population of DO mice in which we imputed local epigenetic state. In contrast, we found that DNA methylation did not vary across inbred strains and was not correlated with variation in expression in DO mice. This work suggests that chromatin state is highly influenced by local genotype and may be a primary mode through which expression quantitative trait loci (eQTLs) are mediated. We further demonstrate that strain variation in chromatin state, paired with gene expression is useful for annotation of functional regions of the mouse genome. Finally, we provide a data resource that documents variation in chromatin state across genetically distinct individuals.
Project description:Mouse inbred strains differ in many aspects of their phenotypes, and it is known that gene expression does so too. This gives us an opportunity to isolate the genetic aspect of variation in expression and compare it to other phenotypic variables. We have investigated these issues using an eight-strain expression profile comparison with four replicates per strain on Affymetrix MGU74av2 GeneChips focusing on one well-defined brain tissue (the hippocampus). We identified substantial strain-specific variation in hippocampal gene expression, with more than two hundred genes showing strain differences by a very conservative criterion. Many such genetically driven differences in gene expression are likely to result in functional differences including differences in behaviour. A large panel of inbred strains could be used to identify genes functionally involved in particular phenotypes, similar to genetic correlation. The genetic correlation between expression profiles and function is potentially very powerful, especially given the current large-scale generation of phenotypic data on multiple strains (the Mouse Phenome Project). As an example, the strongest genetic correlation between more than 200 probe sets showing significant differences among our eight inbred strains and a ranking of these strains by aggression phenotype was found for Comt, a gene known to be involved in aggression. Keywords: mouse, inbred strains, hippocampus, genetic comparison
