Gene expression profiling of the striatum in drug naïve Diversity Outbred mice
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PROVIDER: PRJNA682791 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:416 J:DO drug naïve striatum were subjected to RNA sequencing towards profiling gene expression in these drug naïve straitums.
2021-10-31 | GSE162732 | GEO
Project description:To understand the genetic regulation of gene expression and patterns of gene co-expression, we sequenced the transcriptome of the hippocampus of 258 Diversity Outbred (DO) mice of both sexes. DO mice (fourth and fifth generations of outcrossing) were sacrificed between 6-8 weeks of age and hippocampus dissected. Total hippocampal RNA was isolated using a TRIzol Plus RNA purification kit (Life Technologies) and mRNA sequencing library was prepared using a TruSeq kit (Illumina), both according to manufacturer's protocols. Paired-end 100bp reads were obtained using the Illumina HiSeq 2000.
2019-05-01 | E-MTAB-7637 | biostudies-arrayexpress
Project description:Diversity Outbred Liver RNASeq
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Project description:We measured genome-wide chromatin accessibility of embryonic stem cells derived from Diversity Outbred mice. We cultured cells in media with LIF + GSK3-beta inhibitor CHIR99021.
2020-08-13 | E-MTAB-8759 | biostudies-arrayexpress
Project description:To identify the molecular mechanisms that may initiate therapeutic effects, whole-genome expression profiling (Illumina Mouse WG-6 microarrays) of drug-induced alterations in the mouse brain was undertaken, with a focus on the time-course (1, 2, 4 and 8h) of gene expression changes produced by eighteen major psychotropic drugs: antidepressants, antipsychotics, anxiolytics, psychostimulants and opioids. The resulting database is freely accessible at www.genes2mind.org. Bioinformatics approaches led to the identification of three main drug-responsive genomic networks and indicated neurobiological pathways that mediate the alterations in transcription. Each tested psychotropic drug was characterized by a unique gene network expression profile related to its neuropharmacological properties. Functional links that connect expression of the networks to the development of neuronal adaptations (MAPK signaling pathway), control of brain metabolism (adipocytokine pathway), and organization of cell projections (mTOR pathway) were found. The additional data-sets are available at GEOX1 and GEOX2. The microarray experiment was performed to analyze time-course of drug-induced transcriptional response in C57BL/6J mouse striatum. Three antidepressants (imipramine 10 mg/kg, fluoxetine 20 mg/kg and tianeptine 20 mg/kg, i.p.) were selected for the comparison. Drug doses were previously reported as effective in mice and further tested in our laboratory. To analyze dynamics of early, intermediate and relatively late changes of mRNA abundance the experiment was performed in four time points (1, 2, 4 and 8h after drug administration). To exclude influence of drug injection and circadian rhythm on gene expression profile, control groups of saline treated and naïve animals were prepared for each time point. Design of the experiment assumed pooling of two animals per each array and using of three independent arrays per group. To provide appropriate balance in the whole dataset groups were equally divided between the array hybridization batches.
2013-07-18 | E-GEOD-48951 | biostudies-arrayexpress
Project description:To identify the molecular mechanisms that may initiate therapeutic effects, whole-genome expression profiling (Illumina Mouse WG-6 microarrays) of drug-induced alterations in the mouse brain was undertaken, with a focus on the time-course (1, 2, 4 and 8h) of gene expression changes produced by eighteen major psychotropic drugs: antidepressants, antipsychotics, anxiolytics, psychostimulants and opioids. The resulting database is freely accessible at www.genes2mind.org. Bioinformatics approaches led to the identification of three main drug-responsive genomic networks and indicated neurobiological pathways that mediate the alterations in transcription. Each tested psychotropic drug was characterized by a unique gene network expression profile related to its neuropharmacological properties. Functional links that connect expression of the networks to the development of neuronal adaptations (MAPK signaling pathway), control of brain metabolism (adipocytokine pathway), and organization of cell projections (mTOR pathway) were found. The additional data-sets are available at GEOX1 and GEOX2. The microarray experiment was performed to analyze time-course of drug-induced transcriptional response in C57BL/6J mouse striatum. Three antidepressants (bupropion 20 mg/kg, tranylcypromine 20 mg/kg, mianserin 20 mg/kg, i.p.), three anxiolytics (diazepam 5 mg/kg, buspirone 10 mg/kg, hydroxyzine 10 mg/kg, i.p.), and three antipsychotics (clozapine 3 mg/kg, risperidone 0.5 mg/kg, haloperidol 1 mg/kg) were selected for the comparison. Drug doses were previously reported as effective in mice and further tested in our laboratory. To analyze dynamics of early, intermediate and relatively late changes of mRNA abundance the experiment was performed in four time points (1, 2, 4 and 8h after drug administration). To exclude influence of drug injection and circadian rhythm on gene expression profile, control groups of saline or tween (1% Tween 80) treated and naïve animals were prepared for each time point. Design of the experiment assumed pooling of two animals per each array and using of three independent arrays per group. To provide appropriate balance in the whole dataset groups were equally divided between the array hybridization batches.
2013-07-18 | E-GEOD-48954 | biostudies-arrayexpress
Project description:We measured genome-wide gene expression of embryonic stem cells derived from Diversity Outbred mice. We cultured cells in media with LIF + GSK3-beta inhibitor CHIR99021. All lines were passage 3-8 when RNA was collected. We obtained RNA-Seq from technical replicate cultures for three cell lines.
2020-08-13 | E-MTAB-7728 | biostudies-arrayexpress
Project description:RNA-Seq of hippocampus in Diversity Outbred mice
| PRJEB31082 | ENA
Project description:The striatum is the interface between dopamine reward signals and cortico-basal ganglia circuits that mediate diverse behavioral functions. Medium spiny neurons (MSNs) constitute the vast majority of striatal neurons and are traditionally classified as direct- or indirect-pathway neurons. However, that traditional model does not explain the anatomical and functional diversity of MSNs. Here, we defined molecularly distinct MSN types in the primate striatum, including (1) dorsal striatum MSN types associated with striosome and matrix compartments, (2) ventral striatum types associated with the nucleus accumbens shell and olfactory tubercle, and (3) an MSN-like type restricted to mu-opioid receptor rich islands in the ventral striatum. These results lay the foundation for achieving cell type-specific transgenesis in the primate striatum and provide a blueprint for investigating circuit-specific processing.
2021-11-01 | GSE167920 | GEO
Project description:Clinicians and researchers are turning towards precision medicine to treat and prevent obesity and diabetes, given the known contributions of genetics to these metabolic diseases and the wide variability reported in response to treatments. Animal models that incorporate the genetic diversity present in the human population may help discover novel genetic contributors to metabolic disease and test potential treatments. We characterized the Diversity Outbred (DO) mouse population as a model in which to study interindividual variability in metabolic disease and investigated the presence of metabolic subgroups within the population. Glucose metabolism was assessed in male Diversity Outbred (DO) mice after consumption of a high-fat diet for 14 weeks and profiled transcriptomic changes in liver, adipose, and muscle—key tissues involved in glucose homeostasis. To identify metabolic subgroups, we applied classification and regression tree analyses to metabolic phenotype measures as well as transcriptomic data. These findings suggest that DO mice exhibit a diversity of metabolic phenotypes that can be segmented into subgroups using a machine learning approach. The metabolic subgroups observed in the DO may be a useful for probing the phenotypic variability in metabolic disease observed in humans.
2022-12-30 | GSE194145 | GEO