Gene expression differences between high and low exploratory genetically identical mice
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE11680 | GEO | 2008/10/08
SECONDARY ACCESSION(S): PRJNA106083
REPOSITORIES: GEO
Similar Datasets
Project description:Genetically identical inbred mice exhibit substantial stable individual variability in exploratory behavior. We used microarrays to look at gene expression differences in the hippocampus in female mice separated by stable differences in exploratory behavior Experiment Overall Design: Balb c/J offspring were briefly separated from mothers for 15 minutes each morning on postnatal days 1-14 (handled group) or left undisturbed. At 8 weeks of age mice were tested in the open-field and light-dark behavioral paradigms to verify a handling-induced behavioral phenotype. 2 weeks after behavioral testing, animals were sacrificed and the CA1 region was microdissected. CA1 regions were stored at -20C in RNA later. RNA was extracted from 8 samples (4 handled and 4 non-handled) using Trizol. RNA was extracted from second group of animals (7 handled and 10 non-handled) using Qiagen RNA/DNA columns. All total RNA samples were double round amplied and labeled using standard Affymetrix protocols and hybridized to Mouse 430_2.0 arrays in parallel.
2008-10-26 | E-GEOD-11680 | biostudies-arrayexpress
Project description:NHGRI Clinical Sequencing Exploratory Research Program
| PRJNA158503 | ENA
Project description:Comparison of female and male Daphnia magna gene expression with age. The sexes in Daphnia magna are genetically identical. The aim of this study was to identify possible differences in gene expression between genders with age.
2020-09-23 | GSE125466 | GEO
Project description:Background Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and male Daphnia pulex under controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders. Results In this study we demonstrate that gene expression level is positively correlated with increased DNA methylation, and histone H3 trimethylation at lysine 4 (H3K4me3) at predicted promoter regions. Conversely, elevated histone H3 trimethylation at lysine 27 (H3K27me3), distributed across the entire transcript length, is negatively correlated with gene expression level. Interestingly, male Daphnia are dominated with epigenetic modifications that globally promote elevated gene expression, while female Daphnia are dominated with epigenetic modifications that reduce gene expression globally. For examples, CpG methylation (positively correlated with gene expression level) is significantly higher in almost all differentially methylated sites in male compared to female Daphnia. Furthermore, H3K4me3 modifications are higher in male compared to female Daphnia in more than 3/4 of the differentially regulated promoters. On the other hand, H3K27me3 is higher in female compared to male Daphnia in more than 5/6 of differentially modified sites. However, both sexes demonstrate roughly equal number of genes that are up-regulated in one gender compared to the other sex. Since, gene expression analyses typically assume that most genes are expressed at equal level among samples and different conditions, and thus cannot detect global changes affecting most genes. Conclusions The epigenetic differences between male and female in Daphnia pulex are vast and dominated by changes that promote elevated gene expression in male Daphnia. Furthermore, the differences observed in both gene expression changes and epigenetic modifications between the genders relate to pathways that are physiologically relevant to the observed phenotypic differences.
2019-10-18 | GSE124427 | GEO
Project description:This study aimed to look for transcriptional differences between stage-matched thymic T cell subsets isolated from wildtype and condensin II mutant mice CD4+CD8+ cells from 8-12 week animals were separated according to the expression of CD71, in order to isolate proliferative and non-proliferative subsets
2015-09-01 | GSE65199 | GEO
Project description:Postnatal handling in rodents leads to decreased anxiety-like behavior in adulthood. We used microarrays to look at gene expression differences in the CA1 region of the hippocampus in female mice subjected to postnatal handling compared to controls.
2008-10-08 | GSE11679 | GEO
Project description:Genetic variation in the population has an influence on the manifestation of monogenic as well as multifactorial disorders, with the underlying genetic contribution dependent on several interacting variants. Common laboratory mouse strains used for modelling human disease lack the genetic variability of the human population. Therefore, outcomes of rodent studies show limited correlation with human disease. The functionality of brain vasculature is an important modifier of brain diseases. Importantly, the restrictive interface between blood and brain – the blood-brain barrier (BBB) serves as a major obstacle for CNS drug delivery. Using genetically diverse mouse strains, we aimed to investigate the phenotypic and transcriptomic variation of the intact BBB in different inbred mouse strains.We investigated the heterogeneity of brain vasculature in recently wild-derived mouse strains (CAST/EiJ, WSB/EiJ, PWK/PhJ) and long-inbred mouse strains (129S1/SvImJ, A/J, C57BL/6J, DBA/2J, NOD/ShiLtJ) using different phenotypic arms. We used immunohistochemistry and confocal laser microscopy followed by quantitative image analysis to determine vascular density and pericyte coverage in two brain regions – cortex and hippocampus. Using a low molecular weight fluorescence tracer, sodium fluorescein and spectrophotometry analysis, we assessed BBB permeability in young and aged mice of selected strains. For further phenotypic characterization of endothelial cells in inbred mouse strains, we performed bulk RNA sequencing of sorted endothelial cells isolated from cortex and hippocampus. We did not detect differences in cortical and hippocampal vessel density and pericyte coverage among all the investigated strains. The staining patterns of endothelial arteriovenous zonation markers were similar in different strains. BBB permeability to a small fluorescent tracer, sodium fluorescein, was also similar in different strains. Transcriptomic analysis of endothelial cells revealed that sex of the animal was a major determinant of gene expression differences. In addition, the expression level of several genes implicated in endothelial function and BBB biology differed between wild-derived and long-inbred mouse strains. Our analysis shows that although there were no major differences in parenchymal vascular morphology and BBB permeability between investigated mouse strains or sexes, transcriptomic differences of brain endothelial cells point to variation in gene expression of the intact BBB. These baseline variances might be confounding factors in pathological conditions that may lead to a differential functional outcome dependent on the sex or genetic polymorphism.
2021-08-03 | GSE173793 | GEO
Project description:Postnatal handling in rodents leads to decreased anxiety-like behavior in adulthood. We used microarrays to look at gene expression differences in the CA1 region of the hippocampus in female mice subjected to postnatal handling compared to controls. Experiment Overall Design: Balb c/J offspring were briefly separated from mothers for 15 minutes each morning on postnatal days 1-14 (handled group) or left undisturbed. At 8 weeks of age mice were tested in the open-field and light-dark behavioral paradigms to verify a handling-induced behavioral phenotype. 2 weeks after behavioral testing, animals were sacrificed and the CA1 region was microdissected. CA1 regions were stored at -20C in RNA later. RNA was extracted from 8 samples (4 handled and 4 non-handled) using Trizol. RNA was extracted from second group of animals (7 handled and 10 non-handled) using Qiagen RNA/DNA columns. All total RNA samples were double round amplied and labeled using standard Affymetrix protocols and hybridized to Mouse 430_2.0 arrays in parallel.
2008-10-26 | E-GEOD-11679 | biostudies-arrayexpress
Project description:Innate differences in human temperament strongly influence how individuals cope with stress and predispose for specific types of psychopathology. The present study examines the developing brain in an animal model of temperamental differences to understand how altered neurodevelopment may engender differences in emotional reactivity that are stable throughout the animal’s life. We utilize selectively-bred High Responder (bHR) and Low Responder (bLR) rats that exhibit dramatic emotional behavior differences, with bHRs exhibiting exaggerated novelty-exploration, aggression, impulsivity and drug self-administration, and bLRs showing marked behavioral inhibition, exaggerated anxiety- and depressive-like behavior. Using Affymetrix microarrays, we assessed bLR/bHR gene expression in the developing brain on postnatal days (P)7, 14, and 21, focusing on the hippocampus and nucleus accumbens, two regions related to emotionality and known to differ in adult bLR/bHR rats. We found dramatic bLR/bHR gene expression differences in the P7 and P14 hippocampus, with minimal differences in the nucleus accumbens. Some of the most profound differences involved genes critical for neurodevelopment and synaptogenesis. Stereological studies evaluated hippocampal structure in developing bHR/bLR pups, revealing enhanced hippocampal volume and cell proliferation in bLR animals. Finally, behavioral studies showed that the bHR/bLR behavioral phenotypes emerge very early in life, with exploratory differences apparent at P16 and anxiety differences present by P25. Together these data point to specific brain regions and critical periods when the bHR/bLR phenotypes begin to diverge, which may eventually allow us to test possible therapeutic interventions to normalize extreme phenotypes (e.g. the anxiety-prone nature of bLRs or drug addiction proclivity of bHRs).
2011-12-31 | GSE29552 | GEO
Project description:Innate differences in human temperament strongly influence how individuals cope with stress and predispose for specific types of psychopathology. The present study examines the developing brain in an animal model of temperamental differences to understand how altered neurodevelopment may engender differences in emotional reactivity that are stable throughout the animal’s life. We utilize selectively-bred High Responder (bHR) and Low Responder (bLR) rats that exhibit dramatic emotional behavior differences, with bHRs exhibiting exaggerated novelty-exploration, aggression, impulsivity and drug self-administration, and bLRs showing marked behavioral inhibition, exaggerated anxiety- and depressive-like behavior. Using Affymetrix microarrays, we assessed bLR/bHR gene expression in the developing brain on postnatal days (P)7, 14, and 21, focusing on the hippocampus and nucleus accumbens, two regions related to emotionality and known to differ in adult bLR/bHR rats. We found dramatic bLR/bHR gene expression differences in the P7 and P14 hippocampus, with minimal differences in the nucleus accumbens. Some of the most profound differences involved genes critical for neurodevelopment and synaptogenesis. Stereological studies evaluated hippocampal structure in developing bHR/bLR pups, revealing enhanced hippocampal volume and cell proliferation in bLR animals. Finally, behavioral studies showed that the bHR/bLR behavioral phenotypes emerge very early in life, with exploratory differences apparent at P16 and anxiety differences present by P25. Together these data point to specific brain regions and critical periods when the bHR/bLR phenotypes begin to diverge, which may eventually allow us to test possible therapeutic interventions to normalize extreme phenotypes (e.g. the anxiety-prone nature of bLRs or drug addiction proclivity of bHRs). 2x2x3 factorial design with N=6 per group. Factors as follows: 1) Two selectively bred strains of rats (derived from an original Sprague Dawley population) termed High Responders (HR) and Low Responders (LR), 2) Two brain regions, Hippocampus (HPC) and Nucleus Accumbens (N.Acc), 3) Three developmental timepoints, specifically postnatal days 7 (P7), 14 (P14) and 21 (P21).
2011-12-31 | E-GEOD-29552 | biostudies-arrayexpress