E-GEOD-7762
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA99893
PROVIDER: E-GEOD-7762 | ExpressionAtlas | 2014-08-16
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-7762-analysis-methods.tsv | Tabular | |||
| E-GEOD-7762-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-7762-configuration.xml | Xml | |||
| E-GEOD-7762-configuration.xml.beforeQC | Xml | |||
| E-GEOD-7762-percentile-ranks.tsv | Tabular |
Items per page: 5 1 - 5 of 120 |
Similar Datasets
Project description:Anterior pituitary glands were isolated from 21 week old male rats either untreated or treated for 12 weeks with the synthetic estrogen diethylstilbestrol (DES). Three biological replicates were prepared for untreated, control animals and four biological replicates were prepared for DES-treated animals. This was done for each of 3 inbred rat strains: ACI, Copenhagen, and Brown Norway. Expression profiles were determined using Affymetrix Rat Genome 230 v. 2.0 arrays. Comparisons of untreated vs. treated animals within a strain will allow identification of estrogen responsive genes. Comparisons between strains, either treated or untreated, will identify strain (i.e., genetic) differences in expression. Keywords: Estrogen Response
2006-03-31 | GSE4028 | GEO
Project description:Anterior pituitary glands were isolated from 21 week old male rats either untreated or treated for 12 weeks with the synthetic estrogen diethylstilbestrol (DES). Three biological replicates were prepared for untreated, control animals and four biological replicates were prepared for DES-treated animals. This was done for each of 3 inbred rat strains: ACI, Copenhagen, and Brown Norway. Expression profiles were determined using Affymetrix Rat Genome 230 v. 2.0 arrays. Comparisons of untreated vs. treated animals within a strain will allow identification of estrogen responsive genes. Comparisons between strains, either treated or untreated, will identify strain (i.e., genetic) differences in expression. Experiment Overall Design: 21 samples from anterior pituitary gland were analyzed. For each of 3 inbred rat strains (ACI, Copenhagen, and Brown Norway) there were 3 biological replicates of untreated, control animals, and 4 biological replicates of DES-treated animals.
2009-01-09 | E-GEOD-4028 | biostudies-arrayexpress
Project description:Natural variation in protein expression is common in all organisms and contribute to phenotypic differences among individuals. While variation in gene expression at the transcript level has been extensively investigated, the genetic mechanisms underlying variation in protein expression have lagged considerably behind. Here we investigate genetic architecture of protein expression by profiling a deep mouse brain proteome of two inbred strains, C57BL/6J (B6) and DBA/2J (D2), and their reciprocal F1 hybrids using two-dimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) technology. By comparing protein expression levels in the four mouse strains, we observed 329 statistically significant differentially expressed proteins between the two parental strains and identified four common inheritance patterns, including dominant, additive, over- and under-dominant expression. We further applied the proteogenomic approach to detect variant peptides and define protein allele-specific expression (pASE).
2021-11-01 | PXD025830 | Pride
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
2010-01-28 | GSE17955 | GEO
Project description:Morphine effects on striatal transcriptome in four inbred mouse strains
| PRJNA99893 | ENA
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.
2022-09-25 | GSE213965 | GEO
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.
2010-03-03 | GSE18045 | GEO
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. Four test samples and one reference sample - common reference design- dye swap - 5 to 6 replicates per sample - test samples pooled from 4-6 animals , 23 arrays
2010-05-06 | E-GEOD-18045 | biostudies-arrayexpress
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
2006-08-07 | GSE5429 | GEO
Project description:Chronic opiate use produces molecular and cellular adaptations in the nervous system, leading to tolerance, physical dependence and addiction. Genome-wide comparison of morphine-induced changes in brain transcription of mouse strains with different opioid-related phenotypes provides an opportunity to discover the relationship between gene expression and behavioral response to the drug. Experiment Overall Design: Microarray experiment was designed to determine the impact of genetic background on the transcriptional effects of morphine in the striatum. The effects of single (20 mg/kg, s.c.) and repeated morphine administration (10-40 mg/kg, 3 times daily for 5 days) were analyzed in four inbred mouse strains (129P3/J. DBA/2J, C57BL/6J, SWR/J). Twelve experimental groups were compared. Control animals received injections of saline. Three independent biological replicates of the microarray were prepared for each experimental group. For each array, independent pools of total RNA from three animals were prepared.
2009-02-07 | E-GEOD-7762 | biostudies-arrayexpress