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RNA-Seq of hippocampus in Diversity Outbred mice

ABSTRACT: RNA-Seq of hippocampus in Diversity Outbred mice

PROVIDER: PRJEB31082 | ENA |

REPOSITORIES: ENA

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RNA-Seq of hippocampus in Diversity Outbred mice

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

RNA-Seq of Diversity Outbred mouse embryonic stem cells

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

ATAC-Seq of Diversity Outbred mouse embryonic stem cells

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

Mus musculus strain:Diversity Outbred

Project description:Diversity Outbred Liver RNASeq

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Metabolic subgroups of Diversity Outbred mice show distinct phenotypic and transcriptomic signatures of obesity and insulin resistance

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

Single-cell RNA-seq of bone marrow-derived stromal cells from 5 Diversity Outbred mice

Project description:Genome-wide association studies (GWASs) for osteoporotic traits have identified over 1000 associations; however, their impact has been limited by the difficulties of causal gene identification and a strict focus on bone mineral density (BMD). Here, we used Diversity Outbred (DO) mice to directly address these limitations by performing the first systems genetics analysis of over 50 complex skeletal phenotypes. We applied a network approach to cortical bone RNA-seq data to discover 46 genes likely to be causal for human BMD GWAS associations, including the novel genes SERTAD4 and GLT8D2. We also performed GWAS in the DO for a wide-range of bone traits and identify Qsox1 as a novel gene influencing cortical bone accrual and bone strength. Our results provide a new perspective on the genetics of osteoporosis and highlight the ability of the mouse to inform human genetics.

2020-06-20 | GSE152806 | GEO

RNA-Seq of Diversity Outbred mouse embryonic stem cells

Project description:RNA-Seq of Diversity Outbred mouse embryonic stem cells

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Single-cell RNA-seq of bone marrow-derived stromal cells from 5 Diversity Outbred mice

Project description:Single-cell RNA-seq of bone marrow-derived stromal cells from 5 Diversity Outbred mice

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Gene expression profiling of the striatum in drug naïve Diversity Outbred mice

Project description:Gene expression profiling of the striatum in drug naïve Diversity Outbred mice

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ATAC-Seq of Diversity Outbred mouse embryonic stem cells

Project description:ATAC-Seq of Diversity Outbred mouse embryonic stem cells