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ATAC-Seq of Diversity Outbred mouse embryonic stem cells

ABSTRACT: ATAC-Seq of Diversity Outbred mouse embryonic stem cells

PROVIDER: PRJEB36566 | ENA |

REPOSITORIES: ENA

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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

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

RNA-Seq of Diversity Outbred mouse embryonic stem cells

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

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Mus musculus strain:Diversity Outbred

Project description:Diversity Outbred Liver RNASeq

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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

ATAC-seq of mouse embryonic stem cells

Project description:To identify the accessible chromatin in wild-type mouse embryonic stem cells (mESCs), we performed ATAC-seq in mESCs.

2021-01-05 | E-MTAB-9245 | biostudies-arrayexpress

Project description:SAGA and ATAC are two related transcriptional coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development but the precise role of the two complexes in RNA polymerase II transcription in mammals is less understood. To determine whether SAGA and ATAC have redundant or specific functions dependent on their HAT activities, we compared the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC subunits are required for complex assembly, mouse ESC growth and self-renewal. Additionally, ATAC, but not SAGA subunits are required for ESC viability by regulating the transcription of translation-related genes. Surprisingly, depletion of specific or shared HAT module subunits caused a global decrease in histone H3K9 acetylation, but did not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for viability and self-renewal of mouse ESCs by regulating transcription through different pathways, in a HAT-independent manner.

2021-08-11 | PXD027026 | Pride

ATAC-seq of mouse embryonic stem cells

Project description:ATAC-seq of mouse embryonic stem cells

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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

RNA-Seq of hippocampus in Diversity Outbred mice

Project description:RNA-Seq of hippocampus in Diversity Outbred mice

| PRJEB31082 | ENA