Project description:Genome-wide expression data were generated for polymorphonuclear neutrophils (granulocytes, GN) across 39 strains in the MPD “Priority Strain Panel”.
Project description:Genome-wide expression data were generated for CD3+CD4+CD62L+ naïve T splenocytes across 39 strains in the MPD “Priority Strain Panel”.
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: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. For each inbred strain of mice, CD4+ TCRb+ CD25hi Treg cells (50k) from 9w old male (Jackson laboratory) were double sorted into Trizol. For BM Treg, cells were triple-sorted. Top 50% among CD25high cells were selected to ensure high Foxp3+ purity (over 99%). 2 biological replicates per condition. RNA was amplified, labeled and hybridized to Affymetrix Mouse Gene 1.0 ST Arrays (Expression Analysis).
Project description:Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background Comparison of whole genome expression data of amygdala and hippocampus of both C57BL/6J and A/J mouse inbred strains using a network approach
Project description:Survey of gene expression in 7 brain regions at 6-8wks of age in 20 inbred strains of laboratory mice. Autism is a highly heritable neurodevelopmental disorder with no consistent neuropathological hallmarks, diagnosed through behavioral inventory rather than a biomarker. The genetic etiology of autism is complex and likely has a significant interaction with the environment. To investigate the molecular and genetic nature of autism, we modeled the core symptom of social deficits in inbred strains of mice. Using gene expression profiles and behavioral phenotyping relevant to social deficits, we have identified basic cellular functions that may be dysregulated in the brain in autism. Correlations between these two complex datasets indicate cell morphology, proliferation, and migration may be perturbed in disorders of altered social behavior. Furthermore, these data in the mouse show significant overlap with published expression profiling in lymphoblastoid lines from autistic individuals. Keywords: Comparison between inbred strains and brain regions.
Project description:Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly by comparing the presence or absence of orthologous genes. Due to the high genetic variability, available genotype-calling algorithms can not be applied to pangenome CGH data. Therefore, we have developed the algorithm PanCGH that incorporates orthology information about genes to predict the presence or absence of orthologous genes in a query organism using CGH arrays that target the genomes of sequenced representatives of a group of microorganisms. PanCGH was tested and applied in the analysis of genetic diversity among 39 Lactococcus lactis strains from three different subspecies (lactis, cremoris, hordniae) and isolated from two different niches (dairy and plant). Clustering of these strains using the presence/absence data of gene orthologs revealed a clear separation between different subspecies and reflected the niche of the strains. Keywords: CGH, CGH analysis, orthology, Lactococcus lactis