Gene expression profile in Liver of young and old mice with MANF overexpression
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ABSTRACT:
PROVIDER: PRJNA507596 | ENA |
REPOSITORIES: ENA
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Project description:MANF overexpression in old mice had a beneficial effect in the liver and restored expression levels of several metabolic genes.
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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.
2019-12-31 | GSE113745 | GEO
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
2014-10-23 | E-GEOD-58005 | biostudies-arrayexpress
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 PPARα, PPARγ, and LXRα 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 PPARα targets contributing to gene expression changes that lead to steatosis in aged liver. Genome-wide expression profiles (RNA-Seq) from young (3 months) and old (21 months) mouse livers
2014-10-23 | E-GEOD-57809 | biostudies-arrayexpress
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
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 2259 nuclei prepared from 3 young liver tissues and 2490 nuclei from 3 old liver tissues.
2023-11-09 | E-MTAB-12560 | biostudies-arrayexpress
Project description:Mass spectrometry was performed with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Scientific) interfaced with an UltiMate 3000 Binary RSLCnano System (Dionex). Proteome Discoverer v.1.4 (Thermo Scientific) with SEQUEST HT search engines was used for the spectra-preprocessing and HCD MS2 spectra were used for peptide identification and quantitation based on TMT reporter ions. TMT isobaric comparison of old versus young haematopoietic stem and progenitor cells. Young 1 and Young 2 are samples 126 and 128 of dataset UTH_1. Old 1 and Old 2 are samples 129 and 130 of UTH_1. Young 3 is sample 131 and Old 3 is sample 130 of dataset UTH_4.
2023-10-16 | MSV000093126 | MassIVE
Project description:To find out possible pathways and processes influenced by DmMANF we compared the changes in MANF null and overexpressing animals. We used two developmental stages of Drosophila, st 17 embryos and 29-50 hrs after egg laying (AEL) larvae. The timing were decided according to the lethality of MANF mutants with or without maternal contribution of MANF. Maternal and zygotic MANF mutants (MANFmzD96) were compared to paternal rescue and wild type embryos of the same age. Zygotic MANF mutants (MANFD96) with maternal contribution were compared to wild type and MANF ectopic overexpression larvae harvested well before the average lethality occured (75 hrs AEL). The changes in expression profiles were more drastic in MANFmzD96 embryos than in MANFD96 larvae. Gene ontology annotations were analyzed and clustered by DAVID. The major result was alterations in membranes, changes in membrane transporter expressions and disturbed intracellular membrane traffic. The results were verified by qPCR and transmission electron microscopy. Two developmental stages - 21-24 hrs and 29-50 hrs AEL of MANFD96 mutants without and with maternal contribution were compared to wild type (Wmix means crossed w1118 x w- ) and with paternal rescue or ectopic overexpression of MANF respectively by Drosophila Agilent microarray expression platform.
2012-04-19 | E-GEOD-28820 | biostudies-arrayexpress