Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metabolic profilings of rat INS-1 β-cells under changing levels of essential amino acids

ABSTRACT:

Application of mass spectrometry enables the detection of metabolic differences between organisms with different nutritional settings. Divergence in the metabolic fingerprints of rat pancreatic INS-1 β-cells were systematically captured with regard to 10 individual essential amino acid (EAA) availability. A high-resolution tandem mass spectrometry system coupled to liquid chromatography produced a horizontal comparison of metabolic profilings of β-cells with individual EAA elevated to 10 mmol/L by turn or removal individual EAA from the medium one by one. Quality control samples were injected at regular intervals throughout the analytical run to monitor and evaluate the stability of the system. The raw data of samples and reference compounds including study protocols have been deposited in the open metabolomics database MetaboLights to enable efficient reuse of the datasets, such as investigating the difference in metabolic process between diverse EAAs as well as screening and verifying potential metabolites affecting insulin secretion and β-cell function.

INSTRUMENT(S): Liquid Chromatography MS - positive - hilic, Liquid Chromatography MS - negative - hilic

SUBMITTER: Lianbin Xu

PROVIDER: MTBLS3963 | MetaboLights | 2022-05-24

REPOSITORIES: MetaboLights

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MTBLS3963	Other
	FILES	Other
	a_MTBLS3963_LC-MS_negative_hilic_metabolite_profiling.txt	Txt
	a_MTBLS3963_LC-MS_positive_hilic_metabolite_profiling.txt	Txt
	files-all.json	Other

Items per page:

1 - 5 of 9

Similar Datasets

Genome-wide analysis of renal gene expression during hyperoxaluria development

Project description:Previous studies have proposed that production of reactive oxygen species (ROS) is an important contributor to renal injury and inflammation following exposure to oxalate or calcium-oxalate crystals. The present study was conducted to determine, utilizing global transcriptome analyses, if the NADPH oxidase system is activated in kidneys of rats fed a diet leading to hyperoxaluria and crystal deposition. HLP was used to induce hyperoxaluria. Hyperoxaluria will lead to crystallization and up regulation of various NADPH oxidase subunits followed by increased expression of different specific genes. It is our hypothesis that crystallization induces inflammation of the kidneys via the activation of renin-angiotensin system (RAS) and production of reactive oxygen species (ROS) through NADPH oxidase complex. Apocynin was used to block hyperoxaluria and production of reactive oxygen species (ROS) with the inhibition of NADPH oxidase system as Apocynin inhibits membrane translocation of p47 subunit of NADPH oxidase. The present study was designed based on NADPH oxidase system and rats were divided into 4 groups (n= 6/group). Group 1 was fed regular rat chow diet, Group 2 received regular rat chow diet supplemented with 5% (Hydroxy-L-Proline) HLP, Group 3 received rat chow diet with 4 mmol Apocynin to drink, and Group 4 received regular rat chow diet with 5% HLP and 4 mmol Apocynin. After 28 days each rat was euthanized, their kidneys freshly explanted and dissected to obtain both cortex and medulla tissues. So the 4 groups were divided into cortex and medulla forming 8 groups. RNA was isolated from all the 8 specimens

2012-12-20 | E-GEOD-36446 | biostudies-arrayexpress

Cellular Senescence RT2 Profiler PCR Array of replicative senescent and hyperglycemia treated HUVECs

Project description:Young endothelial cells (CPD >25 and <30; SA-Beta Gal positivity <10%) were exposed to one week of hyperglycemia (25 mmol/L) or sub-cultured until complete growth arrest (CPD > 50). Using real-time PCR, we analyzed the expression of a focused panel of genes involved in cellular senescence.The array includes genes involved in the primary senescence program and known stresses that cause premature senescence.

2017-05-18 | GSE99013 | GEO

Compilation of transcriptomics, non-targeted metabolomics and targeted metabolomics data in bovine mammary epithelial cells stimulated by ten different essential amino acids (Targeted metabolomics)

Project description:Divergence in the targeted amino acid profilings of bovine mammary epithelial cells (BMECs) were systematically captured with regard to 10 individual essential amino acid (EAA) availability. BMECs cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6). DMEM-F12 medium is the positive control treatment (POS), while DMEM-F12 medium devoid of all EAA served as the negative control treatment (NEG). A total of 10 treatments were NEG individually supplemented with arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan or valine. Individual EAA were supplemented to achieve concentrations equal to those of POS. After 6-h treatment, all cell samples were taken at the same time, frozen in liquid nitrogen and stored at -80 °C until required. Targeted metabolomics is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS3956' rel='noopener noreferrer' target='_blank'>MTBLS3956</a>.Untargeted metabolomics is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS7789' rel='noopener noreferrer' target='_blank'>MTBLS7789</a>.

2024-03-04 | MTBLS3956 | MetaboLights

Compilation of transcriptomics, non-targeted metabolomics and targeted metabolomics data in bovine mammary epithelial cells stimulated by ten different essential amino acids (Untargeted metabolomics)

Project description:Divergence in the non-targeted metabolite profilings of bovine mammary epithelial cells (BMECs) were systematically captured with regard to 10 individual essential amino acid (EAA) availability. BMECs cultured in 6-well plates were first serum-starved overnight and subsequently assigned to 1 of 12 treatment media (n = 6). DMEM-F12 medium is the positive control treatment (POS), while DMEM-F12 medium devoid of all EAA served as the negative control treatment (NEG). A total of 10 treatments were NEG individually supplemented with arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan or valine (Sigma-Aldrich, MO, USA). Individual EAA were supplemented to achieve concentrations equal to those of POS. After 6-h treatment, all cell samples were taken at the same time, frozen in liquid nitrogen and stored at -80 °C until required. Untargeted metabolomics is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS7789' rel='noopener noreferrer' target='_blank'>MTBLS7789</a>.Targeted metabolomics is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS3956' rel='noopener noreferrer' target='_blank'>MTBLS3956</a>.

2024-03-04 | MTBLS7789 | MetaboLights

Genome-wide RNAseq of liver tissue derived from humanized mice fed by CDA-HFD and treated with CLDN1 mAb or vehicle Control

Project description:Six-week old Fah−/−/Rag2−/−/Il2rg −/− (FRG) –NOD breeding mice were intravenously injected with 1.5 x 10^9 plaque forming units (pfu) of an adenoviral vector encoding the secreted form of the human urokinase-like plasminogen activator (Ad-uPA). Forty-eight hours later, 10^6 PHH were injected intrasplenically. Successfully transplanted mice were fed with CDA-HFD for 16 weeks and then treated with humanized CLDN1 specific mAb 500 µg or vehicle for additional 8 weeks. RNA was extracted from non-tumorous liver tissue of 4 NASH fibrosis mice treated with CLDN1 mAb, 3 vehicle Control treated NASH fibrosis mice as well as 3 humanized mice fed by regular diet. Libraries were sequenced on the Illumina HiSeq 4000 as Single-Read 50 base reads.

2024-03-12 | GSE174543 | GEO

Epidermal cells help coordinate leukocyte migration during inflammation through fatty acid-fueled matrix metalloproteinase production

Project description:In addition to satisfying the metabolic demands of cells, mitochondrial metabolism helps regulate immune cell function. To date, such cell-intrinsic metabolic-immunologic cross-talk has only been described operating in cells of the immune system. Here we show that epidermal cells utilize fatty acid β-oxidation to fuel their contribution to the immune response during cutaneous inflammation. By live imaging metabolic and immunological processes within intact zebrafish embryos during cutaneous inflammation, we uncover a mechanism where elevated β-oxidation-fueled mitochondria-derived reactive oxygen species within epidermal cells helps guide matrix metalloproteinase-driven leukocyte recruitment. This mechanism requires the activity of a zebrafish homolog of the mammalian mitochondrial enzyme, Immunoresponsive gene 1. This study describes the first example of metabolic reprogramming operating within a non-immune cell type to help control its contribution to the immune response. Targeting of this metabolic-immunologic interface within keratinocytes may prove useful in treating inflammatory dermatoses. In this study, Affymetrix Zebrafish Genome Arrays were used to identify zebrafish Irg1l (a homolog of mammalian IRG1) as a gene up-regulated in response to Salmonella infection. The microarray analysis compared 4 day post fertilisation (dpf) dissected larval zebrafish trunks (approximately 50) that had been injected at 2 dpf with either: (i) PBS (as a negative control) or (ii) live Salmonella enterica serovar Typhimurium bacteria. The study was performed in triplicate.

2014-04-01 | E-GEOD-56365 | biostudies-arrayexpress

Targeting TCA cycle through Cuproptosis confers Synthetic Lethality to ARID1A Deficiency Hepatocellular Carcinoma [ATAC-Seq]

Project description:To further explore the mechanisms of glucose metabolic reprogramming in ARID1A deficiency HCC, we conducted multi-omics profilings in ARID1A deficient and wild type Hep3B cells.

2023-09-07 | GSE228176 | GEO

Targeting TCA cycle through Cuproptosis confers Synthetic Lethality to ARID1A Deficiency Hepatocellular Carcinoma [Cut&Run]

2023-09-07 | GSE228175 | GEO

Analysis of protein expression changes in patients with prediabetes using high-throughput proteomics

Project description:Objective: This study aimed to explore the mechanisms of early-onset T2DM by analyzing proteomic changes at different stages of glucose metabolism. Methods: A total of 40 individuals undergoing routine physical health examinations between December 2016 and April 2017 were enrolled. Subjects were divided into four groups based on fasting blood glucose (FPG) levels: 10 cases with FPG <5.6 mmol/L (group A); 10 cases with FPG ≥5.6 mmol/L and <6.1 mmol/L (group B); 10 cases with FPG ≥6.1 mmol/L and <7.0 mmol/L (group C); and 10 cases with FPG ≥7.0 mmol/L (group D). Results of differential proteomic analysis performed by label-free quantification were compared with metabolites determined by metabolomics. Results: A total of 277 differentially expressed proteins were screened and were identified as mainly secreted proteins. Comparing group A with group B, 32 proteins were up-regulated (fold change >1.2; p <0.05) and 18 proteins were down-regulated (fold change <-1.2; p <0.05). Comparing group B with group C, 3 pro

2022-10-19 | PXD035367 |

Expression data from mouse liver on multisetp-exposure to ethylbenzene

Project description:The processes involved in the adaptation of animals to environmental factors such as chemicals have not yet been fully elucidated. We focused on the adaptive potential of the mouse liver against hepatotoxic chemical-induced injury. We used microarrays to determine genes with adaptive transcriptional regulation against ethylbenzene, hepatotoxic chemical, on multistep-exposure. Four animal groups received the following treatments: phosphate-buffered saline (PBS) followed by PBS (P+P), ethylbenzene followed by PBS (E+P), PBS followed by ethylbenzene (P+E), and ethylbenzene followed by ethylbenzene (E+E). For the first exposure, ethylbenzene (7 mmol kg-1) or PBS (equivalent volume to ethylbenzene) was intraperitoneally injected twice at a 24 h interval. After 7 days of normal feeding, each animal group was treated with ethylbenzene (7 mmol kg-1) or PBS as the secondary exposure. The mice were sacrificed 5 h after the secondary exposure for RNA extraction and hybridization on Affymetrix. The number of mice of each group is as follows, P+P, E+P = 3. P+E, E+E = 5. Specimens from mice of each group were pooled, and 10 μg RNA from each pool was used for cRNA synthesis.

2010-12-25 | E-GEOD-22535 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data