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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Whole Genome oxidative bisulfite sequencing data

ABSTRACT: Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Whole Genome oxidative bisulfite sequencing data

PROVIDER: PRJNA589111 | ENA |

REPOSITORIES: ENA

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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Whole Genome oxidative bisulfite sequencing data

Project description:Studies of neuroepigenetic mechanisms in health and disease are hindered by a lack of approaches to analyze both the transcriptome and epigenome of specific cell types isolated from the complex milieu of the CNS. Cell isolation by cell surface markers is complicated by preparation artifacts, changes in markers with experimental conditions, and lack of specific markers. This study validates a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach with tamoxifen (Tam) inducible cell-type specific cre recombination to allow the parallel interrogation of the epigenome and the transcriptome in astrocytes (Aldh1l1-creERT2) or microglia (Cx3cr1-creERT2). The recombined NuTRAP construct labels, in a cell-type specific manner, nuclei (RanGAP1) with biotin and mCherry, and the ribosomes (L10a) with EGFP, enabling INTACT isolation of DNA and TRAP isolation of RNA. Validation experiments by flow cytometry and imaging demonstrate cell-type specific induction of the NuTRAP construct. Transcriptomic studies demonstrate isolation of highly enriched RNA by TRAP and oxidative bisulfite studies of INTACT-isolated DNA demonstrate differential DNA modification patterns in microglia and astrocytes. LPS administration in Cx3cr1 NuTRAP mice demonstrates that microglia-specific transcriptome and epigenome changes are revealed that cannot be detected with tissue-level samples. These experiments demonstrate that the NuTRAP approach can be applied to CNS cell populations and that INTACT approaches can be used to study DNA modifications. These results also provide an approach for generation and validation of NuTRAP neuroscience models crossed to any relevant cell-type specific cre line.

2020-01-01 | GSE140271 | GEO

Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: RNA-Seq Data

Project description:Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: RNA-Seq Data

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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: LPS Experiment RNA-Seq Data

Project description:Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: LPS Experiment RNA-Seq Data

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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Cx3cr1+ NT+ Hippocampus RNA-Seq Data

Project description:Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Cx3cr1+ NT+ Hippocampus RNA-Seq Data

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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: RNA-Seq Data

2020-01-01 | GSE140895 | GEO

Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia.

Project description:Epigenetic regulation of gene expression occurs in a cell type-specific manner. Current cell-type specific neuroepigenetic studies rely on cell sorting methods that can alter cell phenotype and introduce potential confounds. Here we demonstrate and validate a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach for temporally controlled labeling and isolation of ribosomes and nuclei, and thus RNA and DNA, from specific central nervous system cell types. Analysis of gene expression and DNA modifications in astrocytes or microglia from the same animal demonstrates differential usage of DNA methylation and hydroxymethylation in CpG and non-CpG contexts that corresponds to cell type-specific gene expression. Application of this approach in LPS treated mice uncovers microglia-specific transcriptome and epigenome changes in inflammatory pathways that cannot be detected with tissue-level analysis. The NuTRAP model and the validation approaches presented can be applied to any brain cell type for which a cell type-specific cre is available.

| S-EPMC7678837 | biostudies-literature

Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: LPS Experiment RNA-Seq Data

2020-01-01 | GSE140974 | GEO

Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: Cx3cr1+;NT+ Hippocampus RNA-Seq Data

2020-10-07 | GSE159106 | GEO

Cortical astroglia transcriptomic dysregulation in the G93A SOD1 ALS mouse model

Project description:Astroglia are the most abundant cell type in the central nervous system. They play essential roles in the homeostasis of the CNS. Astroglia are extremely diverse. In Amyotrophic Lateral Sclerosis (ALS) astroglia in spinal cord undergo dramatic transcriptomic dysregulation. However there is little to no data on the effects that cortical astroglia undergo during ALS pathogenesis. In this study we isolated pure cortical astroglia in end stage ALS mice. We performed microarray analysis and discovered dysregulated pathways and genetic markers. This may serve as a database for scientists to understand the effects that abnormal cortical astroglia have on cortical motor neurons and overall ALS pathology.

2019-04-30 | GSE111031 | GEO

DNA methylation and hydroxymethylation assessment through 450K analysis of paired bisulfite and oxidative-bisulfite conversion.

Project description:Analysis of genome-wide hydroxymethylation within infant placental tissue collected at term. These samples have been collected from the RhodeIsland Child Health Study (RICHS) cohort. Bisulfite and oxidative biulfite converted DNA was hybridized to the 450k platform and processed at the University of Minnesota Genomic Core

2016-07-01 | E-GEOD-71719 | biostudies-arrayexpress

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