Haws2025_LiverHistonePTMDataFiles
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Mus Musculus (ncbitaxon:10090)
SUBMITTER: 
John Denu
PROVIDER: MSV000099420 | MassIVE | Wed Oct 08 10:31:00 BST 2025
SECONDARY ACCESSION(S): PXD069207
REPOSITORIES: MassIVE
Similar Datasets
Project description:mzXML files generated from Thermo .raw files of M. musculus liver metabolite extracts following dietary amino acid depletions or rapamycin supplementation. Files were loaded into MAVEN for targeted metabolite quantification.
2025-10-08 | MSV000099424 | MassIVE
Project description:The aim of this study was to explore whether, and if so, how Bacillus subtilis KC1 can enhance the growth performance of broilers that have been adversely affected by Mycoplasma gallisepticum (MG) infection. A total of 96 1-day-old male broilers were randomly divided into 4 groups: the control group (basal diet), the MG group (basal diet + MG challenge), the Bacillus subtilis KC1 group (basal diet + Bacillus subtilis KC1 supplementation), the Bacillus subtilis KC1 + MG group (basal diet + Bacillus subtilis KC1 supplementation + MG challenge). The trial lasted 42 days, and the results showed that the MG group had significantly reduced body weight and average daily gain, as well as increased feed conversion ratio of broilers, compared to the control group. Dietary supplementation with Bacillus subtilis KC1 significantly improved the growth performance of MG-infected broilers. In addition, dietary supplementation with Bacillus subtilis KC1 significantly improved oxidative stress and inflammatory response markers, characterized by increased superoxide dismutase levels and reduced levels of malondialdehyde, interleukin-1β, and tumor necrosis factor-α. Furthermore, both metabolomics and transcriptomics analyses indicated that MG infection markedly disrupted amino acid metabolism in broilers, whereas Bacillus subtilis KC1 supplementation alleviated the abnormal amino acid metabolism caused by MG infection. These results suggested that Bacillus subtilis KC1 may alleviate the poor growth performance caused by MG infection in broilers by improving amino acid metabolism.
2024-10-23 | GSE273913 | GEO
Project description:The study evaluated effects of dietary cholesterol (1.5%) in Atlantic salmon fed a plant based diet for 77 days. Cholesterol supplementation did not affect growth or organ weights of Atlantic salmon, but promoted induction of cholesterol and plant sterol efflux in the intestine, whereas sterol uptake was suppressed. Microarray analyses in the liver indicated decreased cholesterol biosynthesis and enhanced conversion to bile acids. The marked effect of cholesterol on bile acid synthesis suggests that dietary cholesterol can be used to stimulate bile acid synthesis in fish. The study clearly demonstrated how Atlantic salmon adjusted metabolic functions in response to the dietary load of cholesterol, and has expanded our understanding of sterol metabolism and turnover that adds to the knowledge of these processes in fish. Atlantic salmon received feeds based on plant ingredients with (CH) and without (K) supplementation of cholesterol. Liver samples were collected after 77 days. Five individuals from each group were analyzed with microarrays, pooled liver sample of salmon fed with commerical fish meal based feed was used as a reference.
2013-10-31 | E-GEOD-51887 | biostudies-arrayexpress
Project description:Little is known regarding the relationship between Selenium (Se) concentrations in the liver and liver gene expression. Because most cow-calf operations in Se-poor soils provide enough Se in mineral mixes to avoid deficiency, the aim of this study was to determine the effects of 4 Se form supplementation strategies (none or inorganic, organic, or 1:1 inorganic:organic mix) on liver gene expression profiles using a Se-adequate model. Microarray analysis was conducted using the custom WT Btau 4.0 Array (version 1; GeneChip, Affymetrix, Inc., Santa Clara, CA, USA) to determine if dietary Se supplementation form differentially affects the hepatic gene expression profiles of maturing beef heifers. Sodium selenite was used as the source of inorganic Se and Se-enriched yeast was the source of organic selenium. Thirty-six Angus heifers (BW 400 ± 9.0 kg) were ranked on the Se concentration of their biopsied (day -14) liver sample and randomly assigned to one of four dietary Se treatments: Control (Ctrl) group received no exogenous dietary Se supplementation; inorganic (ISe) treatment group received daily dietary Se supplementation at 3 mg/ animal of the ISe form; organic (OSe) treatment group received daily dietary Se supplementation of 3 mg/ animal of OSe form; and the mix (1:1 ISe:OSe) received daily dietary Se supplementation of 3 mg/ animal of 50:50 mix of ISe and OSe forms. RNA was extracted from biopsied liver samples taken 168 days after initiation of Se supplementation and microarray analyses were conducted.
2013-06-01 | E-GEOD-44680 | biostudies-arrayexpress
Project description:Methionine, an essential amino acid, participates in various pathways with implications for the immune system. Recent evidence suggests that it may support both innate and adaptive immune mechanisms. In the present study, it was hypothesized that dietary methionine supplementation prior to vaccination may be a promising strategy to improve vaccine efficacy. Hence, the current research aimed to evaluate the effects of dietary methionine supplementation on the immune status of rainbow trout (Oncorhynchus mykiss) juveniles, its role in modulating immune responses, as well as its potential synergistic effects with a commercial vaccine.
2025-10-21 | PXD068409 | Pride
Project description:Two nutrient sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), control yeast growth and metabolism in response to changes in nutrient availability. Starvation for amino acids activates the GAAC pathway, involving Gcn2p phosphorylation of eIF2 and preferential translation of GCN4, a transcription activator of genes involved in amino acid metabolism. TOR senses nitrogen availability and regulates gene expression through transcription factors, such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome in response to amino acid starvation and rapamycin treatment. Of the ~2500 genes whose expression was changed by 2-fold or greater, Gcn4p and Gln3p were required for 542 and 657 genes, respectively. While Gcn4p activates a common core of 57 genes in response to amino acid starvation or rapamycin treatment, the different stress arrangements allow for variations in Gcn4p-directed transcription. With few exceptions, genes requiring Gcn2p eIF2 kinase for induced expression also required Gcn4p, emphasizing the role of Gcn2p as an upstream activator of Gcn4p-directed transcription. There is also significant coordination between the GAAC and TOR pathways, with Gcn4p being required for activation of more genes during rapamycin treatment than Gln3p. Importantly, TOR regulates the GAAC-directed transcription of genes required for assimilation of nitrogen sources, such as γ-amino-butyric acid. Therefore, yeast has integrated gene expression responses to amino acid abundance and nitrogen source quality through the control of Gcn2p phosphorylation of eIF2 and GCN4 translation. Keywords: gene expression In this study, we carried out microarray analyses in a collection of yeast strains deleted for GCN2, GCN4, and GLN3, individually or in combinations, to explore the importance of the TOR and GAAC pathways in directing the transcriptome in response to amino acid starvation and rapamycin treatment.
2010-03-07 | E-GEOD-15254 | biostudies-arrayexpress
Project description:Zinc (Zn) is an essential trace element for all life forms. Zn supplementation has been used to treat diarrheal disease in children, and in the U.S. swine industry at pharmacological levels to promote growth and fecal consistency, but underlying mechanisms explaining these beneficial effects remain unknown. Thus, we hypothesized that the benefits of pharmacological Zn supplementation were a result of changes in gene expression. For this study, liver RNA from newly weaned pigs fed dietary Zn as Zn oxide for 14 days at either adequate (150 Zn/kg) or pharmacological (2000 mg Zn/kg) levels was evaluated using a 70-mer oligonucleotide microarray. Interrogation of this microarray revealed 658 annotated transcripts (FDR ≤ 0.05) affected by pharmacological Zn supplementation. Relative real-time RT-PCR was used to confirm differential expression of two genes. Results suggest that feeding pharmacological Zn (2000 mg Zn/kg) affects genes involved in reducing oxidative stress and in amino acid metabolism, which are essential for cell detoxification and proper cell function.
2008-10-02 | GSE11972 | GEO
Project description:The above study is an original research that employs transcriptomics analysis to investigate the hypothalamic responses associated with dietary L-Citrulline treatment. L-Citrulline is a non-essential amino acid that is widely gaining research interest due to its role in thermoregulation and its efficiency as an arginine/nitric oxide precursor. Therefore, this study demonstrates that dietary supplementation of L-citrulline to broilers under different housing temperatures would stimulate regulatory pathways involved with brain development and feeding behavior. We have also identified potential candidate genes that would be beneficial in fostering further research on L-citrulline-induced hypothermia.
2022-05-09 | GSE202003 | GEO
Project description:Amino acid starvation during recombinant protein production (RPP) induces metabolic stress to cellular host which results in reduced productivity of the recombinant bioprocess. In present study, supplementation of amino acids in a chemically defined medium showed several folds increase in recombinant product titers in E. coli BL21 DE3 strain. To understand, the effect of amino acid supplementation in alleviating cellular stress during RPP a deep insight of cellular physiology must be studied. Here, we performed transcriptomic analysis of E. coli expressing a recombinant protein in two different conditions: with (5 mM of all 20 amino acids) as test and without supplementation of amino acids as control. RNA-seq data revealed downregulation of several genes associated with stress in test culture confirming the critical role of amino acids supplementation in improving RPP.
2020-05-18 | GSE138044 | GEO
Project description:Purpose: Although the prevalence of non-alcoholic fatty liver disease (NAFLD) continues to increase, there is no effective treatment approved for this condition. We previously showed, in high-fat diet (HFD)-fed mice, that the supplementation of combined metabolic activators (CMA), including nicotinamide riboside (NAD+ precursor) and the potent glutathione precursors serine and N-acetyl-l-cysteine (NAC), significantly decreased fatty liver by promoting fat oxidation in mitochondria. Afterwards, in a one-day proof-of-concept human supplementation study, we observed that this CMA, including also L-carnitine tartrate (LCT), resulted in increased fatty acid oxidation and de novo glutathione synthesis. However, the underlying molecular mechanisms associated with supplementation of CMA have not been fully elucidated. Conclusions: Our study demonstrated in hamsters that the chronic supplementation of this CMA (changing serine for betaine) at two doses significantly decreased hepatic steatosis. We further generated liver transcriptomics data and integrated these data using a liver-specific genome-scale metabolic model of liver tissue. We systemically determined the molecular changes after the supplementation of CMA and found that it activates mitochondria in the liver tissue by modulating global lipid, amino acid, antioxidant and folate metabolism. Our findings provide extra evidence about the beneficial effects of a treatment based on this CMA against NAFLD.
2021-10-22 | GSE186165 | GEO