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ABSTRACT: Single-cell RNA sequencing analysis of the testis of db/db mice

PROVIDER: PRJNA1049622 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27150065.fastq.gz	Fastqsanger.gz
	SRR27150066.fastq.gz	Fastqsanger.gz

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Project description:Single cell RNA sequencing of db/db mice kidney

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Single-cell sequencing analysis of the db/db mouse hippocampus reveals cell-type-specific insights into the pathobiology of diabetes-associated cognitive dysfunction

Project description:Diabetes-associated cognitive decline (DCD) is one of the complications of diabetes, which is characterized by a series of neurophysiological and pathological abnormalities. However, the exact pathogenesis of DCD is still unknown. Single-cell RNA sequencing (scRNA-seq) could discover unusual subpopulations, explore functional heterogeneity and identify signaling pathways and potential markers. The aim of this research was to provide deeper opinion into molecular and cellular changes underlying DCD, identify different cellular types of the diabetic mice hippocampus at single-cell level, and elucidate the factors mediating the pathogenesis of DCD. To elucidate cell specific gene expression changes in the hippocampus of diabetic encephalopathy, single-cell RNA sequencing of hippocampus from db/m and db/db mice was carried out. Subclustering analysis was performed to further describe microglial cell subpopulations. Interestingly using immunohistochemistry, these findings were confirmed at the protein level. Single cell analysis yielded transcriptome data for 14621 hippocampal cells and defined 11 different cell types. Analysis of differentially expressed genes in the microglia compartments indicated that infection- and immune system process- associated terms, oxidative stress and inflammation play vital roles in the progression of DCD. Compared with db/m mouse, experiments at the protein level supported the activation of microglia, increased expression of inflammatory factors and oxidative stress damage in the hippocampus of db/db mouse. In addition, a major finding of our research was the subpopulation of microglia that express genes related to pro-inflammatory disease-associated microglia (DAM). Our research reveals pathological alterations of inflammation and oxidative stress mediated hippocampal damage in the db/db mice, and may provide potential diagnostic biomarkers and therapeutic interventions for DCD.

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Single-cell RNA profiling of the kidney in fructose overdose model using db/db mice

Project description:We have established a new fructose-overconsumption model using db/db mice, which showed more advanced kidney damage compared to the conventional db/db mouse model. To elucidate the mechanism of kidney injury caused by excessive fructose intake, we performed single-cell RNA analysis on the kidneys from this fructose-overconsumption model.

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Gene expression profile at single cell level of skin cells isolated from db/db mice

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Project description:We reported a 28-day Intermittent fasting (IF) regimen improved cognitive deficits in db/db mice via a microbiota-metabolites-brain axis assessed by behavioral tests and multiple-omics analysis (transciptomics, 16S rRNA sequencing and metabolomics). Here we present transcriptomics data of mice hippocampus. A total of 310.85Gb clean RNA-SEQ reads of all mice with an average depth of 3.86x were obtained and were then mapped against the Mus musculus genome to obtain the gene expression FPKM values for each sample. We detected 27,094 genes (including 1,345 new predicted genes with no annotation) with FPKM value. Among them, 1,181 genes were found to be only highly expressed in db/db-IF mice compared to db/db and db/m mice, using Differentially Expressed Genes (DEG) analysis, most of which enriched in mitochondrial-related GO terms. Besides, IF strongly elevated genes related to KEGG pathway of oxidative phosphorylation (OXPHOS) via up-regulating mitochondrial located genes expression. In consistent with results from RNA-sequencing analysis, the qPCR analysis confirmed that mitochondrial and metabolic genes expressed were upregulated by IF in db/db mice. In conclusion, IF regimen significantly enhanced mitochondrial and energy metabolism related genes expressions in diabetic mice hippocampus.

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Project description:Single cell sequencing revealed that the composition of islets cells were changed significantly in db/db mice, indicating diet intervention can shape islets cells and restore the function of endocrine cells in pancreases islets.

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Single-cell RNA profiling of the kidney in fructose overdose model using db/db mice

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Vertical sleeve gastrectomy triggers fast β-cell recovery upon overt diabetes

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