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Single cell RNA-sequencing of NK cells from control wildtype and 3XTg-AD mice

ABSTRACT: The goal of this study is to examine the single-cell transcriptomes of NK cells from the brains of 3XTg-AD and control wildtype mice. The data generated will elucidate the transcriptomal changes of NK cells in the pro-inflammatory microenvironment of mice with Alzheimer's disease pathologies.

ORGANISM(S): Mus musculus

PROVIDER: GSE142853 | GEO | 2020/06/08

REPOSITORIES: GEO

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Bulk RNA-sequencing of microglia in 3XTg-AD mice treated with anti-Nk1.1 depleting antibodies or isotype control

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Transcriptomes of Neural Stem and Progenitor Cells from the subgranular zone (SGZ) of Wild Type (NTG) and 3xTg-AD mice at juvenile age

Project description:The goals of this study are to compare transcriptome profiling (RNA-seq) in wild-type (NTG) and 3xTg-AD mice, to determine the transcriptomal changes of neural stem and progenitor cells (NSPC) from the SGZ at early stages of Alzheimer's Disease in a mouse model. Methods: A tamoxifen (TAM)-inducible Nestin-CreERT2;ROSA26-EYFP reporter mouse line was cross-bred with NTG or 3xTG-AD mice to label NSPC upon TAM administration. YFP-positive NSPCs were sorted through FACS (Fluorescence-Activated Cell Sorting) 10 days after TAM from NTG; Nestin-CreERT2;ROSA26-EYFP and 3xTg-AD;Nestin-CreERT2;ROSA26-EYFP mice. RNA was extracted with RNeasy Micro Kit and deep-sequenced on the NovaSeq SP flowcell SR200 platform. The sequence reads of Fastq files that passed quality filters were aligned to the mouse genome (build mm10) using hisat2. Samtools was used to index the BAM files. DESeq2 was used to establish differential gene expression between NTG and 3xTg-AD samples. Results: We mapped about 48 million sequence reads per sample to the mouse genome (build mm10) and identified 1391 genes that were differentially expressed in the 3xTg-AD, with 720 down- and 671 up-regulated. Genes were considered significantly different between two genotypes if they meet the following criteria: 1) adjusted p-value < 0.05, and 2) log2 fold change > 0.5 or < -0.5. Conclusions: Gene ontology analysis of differentially expressed genes uncovered several pathways that may contribute to early neural stem cell decline in the 3xTg mice. Our results revealed very early perturbations in the SGZ neurogenic niche in the 3xTg mouse model of AD, manifested by intrinsic molecular changes in neural stem and progenitor cells (NSPC) at juvenile age, resulting in dysregulated neural stem cell homeostasis.

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Lateral ventricle SVZ: 3xTg vs WT

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Single cell RNA-sequencing of NK cells from control wildtype and 3XTg-AD mice

Project description:Single cell RNA-sequencing of NK cells from control wildtype and 3XTg-AD mice

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Senescent cell elimination modifies features of Alzheimer’s disease in 3xTg-AD mice

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