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ScRNAseq and TCRseq of hepatic and splenic CD8T cells from normal diet fed (ND), HFHC diet fed (HFHC), and resolution induced (RES) mice.

ABSTRACT: scRNAseq and TCRseq of hepatic and splenic CD8T cells from normal diet fed (ND), HFHC diet fed (HFHC), and resolution induced (RES) mice.

PROVIDER: PRJNA735386 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14740246.fastq.gz	Fastqsanger.gz
	SRR14740247.fastq.gz	Fastqsanger.gz
	SRR14740248.fastq.gz	Fastqsanger.gz
	SRR14740249.fastq.gz	Fastqsanger.gz
	SRR14740250.fastq.gz	Fastqsanger.gz

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scRNAseq and TCRseq of hepatic and splenic CD8T cells from normal diet fed (ND), HFHC diet fed (HFHC), and resolution induced (RES) mice.

Project description:To explore key features associated with the resolution process in liver fibrosis, we here applied a unique murine model, in which mice were fed HFHC diet for 24 weeks, and then continued with the HFHC diet (HFHC) or switched to a normal diet (RES) for 5 weeks. We noted that both the frequency and number of intrahepatic CD8+ T cells remained significantly high in RES mice compared to normal diet-fed mice (ND). To reveal the transcriptome profiling-based subtypes of CD8+T cells present during the liver fibosis resolution, we performed scRNA-seq analysis. Total of 25851 cells were clustered into 17 clusters based on the gene signatures. We revealed CD69+CD103-CD8+ Trm cell enrichment in fibrosis resolution livers. scTCR-seq analysis further revealed the clonal enrichment mainly in the Cd44+Sell-S1pr1- liver Trm fractions. In addition, TCR clonotypes enriched in liver CD8+ Trm cells of RES mice were expanded compared to those in liver CD8+ T cells of ND mice, and rarely detected in spleen CD8+ T cells.

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Changes of hepatic gene expression in C57BL/6N male mice fed high-fat high-calorie fructose (HFHC) diet for 8 weeks

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Identification of eQTLs for Hepatic Xbp1s and Socs3 Gene Expression in Mice fed a High-Fat, High Caloric Diet

Project description:Non-alcoholic fatty liver disease (NAFLD) is a highly prevalent form of hepatic disease and feeding mice a High-Fat, High-Caloric (HFHC) diet is a standard model of NAFLD. In order to better understand the genetic basis of NAFLD, we conducted an expression quantitative trait locus (eQTL) analysis of mice fed a HFHC diet. 265 (A/J × C57BL/6J) F2 male mice were fed a HFHC diet for 8 weeks. QTL analysis was utilized to identify genomic regions that regulate hepatic gene expression of Xbp1s and Socs3. We identified two overlapping loci for Xbp1 and Socs3 on Chr 1 (164.0-185.4 Mb and 174.4-190.5 Mb, respectively) and Chr 11 (41.1-73.1 Mb and 44.0-68.6 Mb, respectively), and an additional locus for Socs3 on Chr 12 (109.9-117.4 Mb). C57BL/6J-Chr 11A/J/ NaJ mice fed a HFHC diet manifested the A/J phenotype of increased Xbp1s and Socs3 gene expression (p<0.05), while C57BL/6J-Chr 1A/J/ NaJ mice retained the C57BL/6 phenotype. In addition, we replicated the eQTLs on Chr 1 and 12 (LOD scores ? 3.5) using mice from the BXD murine reference panel challenged with CCl4 to induce chronic liver injury and fibrosis. We have identified overlapping eQTLs for Xbp1 and Socs3 on Chr 1 and 11, and consomic mice confirmed that replacing the C57BL/6 with the A/J Chr 11 resulted in an A/J phenotype for Xbp1 and Socs3 gene expression. Identification of the genes for these eQTLs will lead to a better understanding of the genetic factors responsible for NAFLD and potentially other hepatic diseases. Liver samples from eight-week-old AJ and C57BL6J males fed a High Fat High Calorie diet.

2014-08-02 | E-GEOD-56987 | biostudies-arrayexpress

Identification of eQTLs for Hepatic Xbp1s and Socs3 Gene Expression in Mice fed a High-Fat, High Caloric Diet

2014-08-02 | GSE56987 | GEO

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Project description:Mice with MUTYH-null allele (Mutyh+/-, Mutyh-/-) were fed a high-fat/high-cholesterol (HFHC) diet or HFHC + high iron diet. The incidence of liver tumors and histological features of the liver were compared. We used microarray to examine the gene expression patterns associated with hepatocarcinogenesis in our model.

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Project description:Proteomics of liver tissue from mice fed a high fat diet (HFD) or regular chow diet. Data accompany our paper entitled “Dynamic Regulation of N6,2′-O-dimethyladenosine (m6Am) in Obesity” scheduled for publication in Nature Communications, 2021

2021-10-27 | PXD029280 | Pride

FUME-TCRseq

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Spleen proteomics data from high fat diet fed mice

Project description:The composition of the diet affects many processes in the body, including body weight and endocrine system. We have previously shown that dietary fat also affects the immune system. Mice fed high fat diet rich in polyunsaturated fatty acids survive S. aureus infection to a much greater extent than mice fed high fat diet rich in saturated fatty acids. Here we present data regarding the dietary effects on protein expression in spleen from mice fed three different diets, I) low fat/chow diet (LFD, n=4), II) high fat diet rich in saturated fatty acids (HFD-S, n=4) and III) high fat diet rich in polyunsaturated fatty acids (HFD-P, n=4). We performed mass spectrophotometry based quantitative proteomics analysis of isolated spleen by implementing the isobaric tags for relative and absolute quantification (iTRAQ) approach. Mass spectrometry data were analysed using Proteome Discoverer 2.4 software using the search engine mascot against Mus musculus in SwissProt. 924 proteins are identified in all sets (n=4) for different dietary effects taken for statistical analysis using Qlucore Omics Explorer software. Only 20 proteins were found to be differentially expressed with a cut-off value of false discovery rate < 0.1 (q-value) when comparing HFD-S and HFD-P but no differentially expressed proteins were found when LFD was compared with HFD-P or HFD-S. We identified a subset of proteins that showed an inverse expression pattern between two high fat diets. These differentially expressed proteins were further classified by gene ontology for their role in biological processes and molecular functions.

2020-08-06 | PXD020365 | Pride

Differential analysis of mitochondria-associated reticulum membranes (MAMs) between standard diet-fed and high fat high sucrose diet fed mice

Project description:Type 2 diabetic cardiomyopathy (DCM) has been linked to Ca2+ signaling alterations, notably a decreased mitochondrial Ca2+ uptake. Uncovering of Ca2+ microdomains between cardiac mitochondria and reticulum launched a new investigation avenue for cardiometabolic diseases. We here aimed to study if the impairment of mitochondrial Ca2+ handling could be due to a dysregulation of the reticulum-mitochondria interactions or of the mitochondrial Ca2+ uniporter in the diabetic mice heart. Phenotypic alterations of the type 2 diabetic mouse heart, was done using an in vivo obesogenic high fat high sucrose diet fed mouse model (HFHSD: 20% proteins, 36% lipids). The composition of the cardiac MAM fractions between standard diet-fed (SD) mice and HFHSD (HF) mice at 16 weeks was analysed by MS-based quantitative proteomics.

2020-12-02 | PXD015280 | Pride

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