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ScATAC-seq of mouse liver tissue derived from young and old mice

ABSTRACT: scATAC-seq of mouse liver tissue derived from young and old mice

PROVIDER: PRJEB59833 | ENA |

REPOSITORIES: ENA

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scATAC-seq of mouse liver tissue derived from young and old mice II

Project description:scATAC-seq of mouse liver tissue derived from young and old mice II

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scATAC-seq of mouse liver tissue derived from young and old mice

Project description:We investigate if the differences in phenotype and transcriptome over age might be explained by an underlying change on the epigenetic level. We performed single-cell ATAC sequencing using the 10x Chromium platform. We profiled 4838 nuclei prepared from 3 young liver tissues and 3361 nuclei from 3 old liver tissues.

2023-02-20 | E-MTAB-12706 | biostudies-arrayexpress

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2023-11-09 | E-MTAB-12560 | biostudies-arrayexpress

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scRNA-seq of mouse liver tissue derived from young and old mice

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scRNA-seq of mouse liver tissue derived from young and old mice

Project description:We want to investigate how cells in the specific zones in murine liver are affected by age-related changes of the microenvironment. To this end, we generated high-quality scRNA-seq dataset of hepatocytes using Smart-seq3express from 2 young (3-5 months) and 2 old (18-20 months) male mice. Livers were perfused and viable hepatocytes were FACS-sorted based on size. In addition, we recorded ploidy levels of hepatocytes. We retained 545 hepatocytes in total after initial filtering.

2023-11-01 | E-MTAB-12579 | biostudies-arrayexpress

RNA-seq of Wistar-rat liver from young and old animals

Project description:Comparison of gene expression level by Illumina sequencing of rat liver from young and old animals. We identified differentially expressed genes and provide functional profiles, which give insights into the aging process of short-lived rodents.

2017-09-19 | GSE98745 | GEO

RNA-seq of naked mole-rat liver from young and old animals

Project description:Comparison of gene expression level by Illumina sequencing of naked mole-rat liver from young and old animals. We identified differentially expressed genes and provide functional profiles, which give insights into the aging process of long-lived rodents.

2018-03-28 | GSE98744 | GEO

RNA-seq reveals differences in liver gene expression rhythms between young and old mice

Project description:Purpose: We used RNA-seq to compare daily rhythms of gene expression in livers of young and old mice. Methods: Livers of young and old mice were processed for RNA-seq at 4-h interval across 2 days. Gene expression level was analyzed by hisat2 and StringTie. Results: We obtained ~10 million high quality sequencing reads per time point per sample after quality control and alignment. Gene expression levels of ~19,000 transcripts were obtained for both age groups. We found genome-wide differenes in gene expression level as well as rhythms in gene expression. Conclusions: Our study revealed genomwide differences in the level and rhythm of liver gene expression between young and old mice.

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Nucleosome occupancy profiles in young and old mouse liver [MNase-Seq]

Project description:Aging is accompanied by physiological impairments, which, in insulin-responsive tissues, including the liver, predispose individuals to metabolic disease. However, the molecular mechanisms underlying these changes remain largely unknown. Here, we analyze genome-wide profiles of RNA and chromatin organization in the liver of young (3 months) and old (21 months) mice. Transcriptional changes suggest that de-repression of the nuclear receptors PPARM-NM-1, PPARM-NM-3, and LXRM-NM-1 in aged mouse liver leads to activation of targets regulating lipid synthesis and storage, whereas age-dependent changes in nucleosome occupancy are associated with binding sites for both known regulators (forkhead factors and nuclear receptors) and for novel candidates associated with nuclear lamina (Hdac3 and Srf) implicated to govern metabolic function of aging liver. Winged-helix factor Foxa2 and nuclear receptor co-repressor Hdac3 exhibit reciprocal binding pattern at PPARM-NM-1 targets contributing to gene expression changes that lead to steatosis in aged liver. Genome-wide nucleosome profiles (MNase-Seq) from young (3 months) and old (21 months) mouse livers

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