Haws2025_LiverMetabolomicsDataFiles
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Mus Musculus (ncbitaxon:10090)
SUBMITTER: 
John Denu
PROVIDER: MSV000099424 | MassIVE | Wed Oct 08 12:21:00 BST 2025
REPOSITORIES: MassIVE
Similar Datasets
Project description:Thermo .raw histone proteomics files of acid extracted histone proteins isolated from M. musculus liver following dietary amino acid depletions or rapamycin supplementation.
2025-10-08 | MSV000099420 | MassIVE
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:Selenium (Se) is an essential nutrient for beef cattle health and commercial production. The molecular mechanisms responsible for physiological responses of the animal to dietary Se supplementation, however, have not been evaluated. Furthermore, the potential effect of two chemical forms (organic vs. inorganic) of Se on gene expression by Se-sufficient cattle has not been evaluated. Microarray analysis using the GeneChip Bovine Genome Array (Affymetrix, Inc., Santa Clara, CA) was conducted to determine if dietary Se supplementation in organic vs. inorganic form (OSe vs. ISe) differentially affects the liver gene expression profile in growing beef heifers. Sodium selenite (Prince Se Concentrate; Prince Agri Products, Inc., Quincy, IL) was used as the source of ISe form. Se-enriched yeast (Sel-Plex; Alltech, Inc., Nicholasville, KY) was used as the source of OSe form. Thirty Angus heifers (BW 393 ± 9 kg) were randomly assigned to 3 dietary treatments (n = 10): Control (Ctrl) group received no dietary Se supplementation; ISe treatment group daily received dietary supplementation of Se at 3 mg/animal from ISe source; OSe treatment group daily received dietary supplementation of Se at 3 mg/animal from OSe source. Six animals were randomly selected from each of 3 treatment groups for RNA extraction and microarray analysis.
2010-04-28 | E-GEOD-19696 | biostudies-arrayexpress
Project description:Purpose: The aim of this study was to evaluate the effect of essentail oil dietary supplementation on gene expression in liver and muscle tissue.
2018-02-14 | GSE110550 | GEO
Project description:Plant-based protein sources play an important role in aquaculture by dwindling fish meal to sustainable levels. However, the use of such feedstuffs requires nutrient supplementation to fulfil fish nutritional requirements. This work addressed the response in the liver of farmed fish to dietary methionine (Met), assessing at the same time the growth performance. Fish were fed at suboptimal levels of dietary Met (0.77% w/w; M0.65 diet), within (1% w/w Met; M0.85 diet)and above(1.36 % w/w Met (M1.25 diet); 1.66% w/w Met(M1.5 diet)) the estimated requirement for this species, in a total of four tested conditions. The impact of dietary methionine supplementation in seabass juvenile’s performance was assessed through 85 days of trial, between May and August of 2018. Fish were reared in triplicate tanks and three liver samples/tank (9 per treatment) were collected for liver proteome analysis at the end of the trial i.e., after 85 days of feeding.
2020-11-25 | PXD019622 | Pride
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:The hypothesis was that 6 months of dietary n-3 FA supplementation to humans affected expression of genes that might be of significance for inflammatory processes and for Alzheimer´s disease. Effects on global gene expression profiles (Affymetrix Human Focus array) in human blood mononuclear leukocytes obtained from 11 patients with Alzheimer´s disease before and after 6 months of a DHA-rich n-3 fatty acid supplementation. Data analyses were performed using Gene chip Operating Software (GCOS) Version 1.4. Two Samples, GSM735991 and GSM736014, are missing CEL files due to storage failure.
2012-05-23 | E-GEOD-29680 | biostudies-arrayexpress
Project description:Plant-based protein sources play an important role in aquaculture by dwindling fish meal to sustainable levels. However, the use of such feedstuffs requires nutrient supplementation to fulfil fish nutritional requirements. This work addressed the response in the liver of farmed fish to dietary methionine (Met), assessing at the same time the growth performance. Fish were fed at suboptimal levels of dietary Met (0.77% w/w; M0.65 diet), within (1% w/w Met; M0.85 diet)and above(1.36 % w/w Met (M1.25 diet); 1.66% w/w Met(M1.5 diet)) the estimated requirement for this species, in a total of four tested conditions. The impact of dietary methionine supplementation in seabass juvenile’s performance was assessed through 85 days of trial, between May and August of 2018. Fish were reared in triplicate tanks and three liver samples/tank (9 per treatment) were collected for liver proteome analysis at the beginning and at the end of the trial i.e., after 18 and 85 days offeeding, correspondingly. This dataset refers to the 18th day of sampling.
2020-12-02 | PXD019610 | Pride
Project description:Tumour cells adapt to nutrient deprivation in vivo, yet strategies targeting the nutrient poor microenvironment remain unexplored. We recently found, in melanoma, tumour cells often experience low glutamine levels, which induce histone hypermethylation, promote dedifferentiation, and increase resistance to BRAF inhibitors. These findings raise the possibility that increased glutamine levels can be detrimental to melanoma tumours. Here, we show that dietary glutamine supplementation significantly inhibits melanoma tumour growth, prolongs survival in transgenic mouse model, and increases sensitivity to BRAF targeted inhibitors in both melanoma xenograft and patient-derived xenograft (PDX) models. Notably, metabolomic analysis reveals that dietary uptake of glutamine effectively increases the concentration of glutamine and its downstream metabolite, αKG, in serum and tumours, without increasing biosynthetic intermediates necessary for cell proliferation. Mechanistically, we find that glutamine supplementation uniformly alters the transcriptome and suppresses expression of many melanoma-associated genes. Our data further demonstrate that increase in intra-tumoural αKG concentration, following glutamine supplementation, drives hypomethylation of H3K4me3, thereby suppressing epigenetically-activated oncogenic pathways in melanoma. Therefore, our findings provide important evidence that glutamine supplementation can serve as a potential dietary intervention to block melanoma tumour growth and sensitize tumours to targeted therapy via epigenetic reprogramming.
2020-05-14 | GSE140274 | GEO