Browse
Submit Data
Databases
API
Help

Dataset Information

236 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome changes during mouse brain aging

ABSTRACT: Analysis of proteome changes during mouse brain aging

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain

SUBMITTER: Jacek Wisniewski

LAB HEAD: Jacek R Wisniewski

PROVIDER: PXD005230 | Pride | 2018-07-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20160630_QEp7_JRW_SA_L_Q100.raw	Raw
	20160630_QEp7_JRW_SA_L_Q101.raw	Raw
	20160630_QEp7_JRW_SA_L_Q102.raw	Raw
	20160630_QEp7_JRW_SA_L_Q103.raw	Raw
	20160630_QEp7_JRW_SA_L_Q104.raw	Raw

Items per page:

1 - 5 of 73

Publications

[Fixation of single crown stumps in elastic rubber impressions].

Brune G G

Die Quintessenz der Zahntechnik 19781201 12

PMID: 399024

Similar Datasets

Changes in glycogen metabolism machinery are associated with brain aging. Proteomic and immunofluorescent evidence for and against the astrocyte-to-neuron lactate shuttle

Project description:Analysis of proteome changes during mouse brain aging

2018-03-05 | PXD006815 | Pride

Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cellsLinking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells

Project description:Background: The Ras pathway genes KRAS, BRAF or ERBBs have somatic mutations in ~60% of human colorectal carcinomas. At present, it is unknown whether the remaining cases lack mutations activating the Ras pathway, or whether they have acquired mutations in genes hitherto not known to belong to the pathway. Methods: To address the second possibility, and extend the compendium of Ras pathway genes, we used genome-wide transposon mutagenesis of two human colorectal cancer cell systems deprived of their activating KRAS or BRAF allele to identify genes enabling growth in low glucose, a Ras pathway phenotype, when targeted. Results: Of the 163 recurrently targeted genes in the two different genetic backgrounds, one third were known cancer genes and one-fifth had links to the EGFR/Ras/MAPK pathway. When compared to cancer genome sequencing datasets, 9 genes also mutated in human colorectal cancers were identified. Among these, stable knock-down of FOXO3, NCOA3, and TCF7L2 restored growth in low glucose but reduced MEK/MAPK phosphorylation, reduced anchorage-independent growth, and modulated expressions of GLUT1 and Ras pathway related proteins. Knock-down of NCOA3 and FOXO3 significantly decreased the sensitivity to cetuximab of KRAS mutant but not wild-type cells. Conclusions: This work establishes a proof-of-concept that human cell based genome-wide forward genetic screens can assign genes to pathways with clinical importance in human colorectal cancer.

2018-02-20 | PXD008382 | Pride

A reference database of electrophoretic migration patterns for human proteins in a set of cell lines.

Project description:Protein denaturing electrophoresis based on sodium dodecyl sulfate (SDS-PAGE) is a technique widely applied for studying proteins, either alone or in combination with specific antibody-based detection. Despite its popularity, SDS-PAGE and western blotting are poorly reproducible and can give different results depending on experimental factors affecting electrophoresis but also on the characteristics of the antibodies used for detection. We reasoned that a reference database of accurately determined migration patterns for human proteins would be very useful for the community. Using mass spectrometry and an internal calibration strategy, we have constructed a database of migration patterns for thousands of proteins in five commonly used human cell lines and one mouse cell line. We show that the electrophoretic molecular weights determined are accurate and, for a large portion of the proteome, highly reproducible across replicates and cell lines. Data exploration highlighted numerous known protein processing events that can be mapped by combining migration patterns and the sequence coverage observed. The information is freely available in a website and should constitute a useful reference for investigators trying to validate western blot results and protein migrations in general.

2023-01-05 | PXD026750 | Pride

Molecular profiling of tumor-derived exosomes in plasma of patients with melanoma

Project description:By isolation of exosomes from body fluids such as serum or plasma with the use of a gel filtration method developed for this purpose, we showed that the level of exosomes in patients with melanoma is higher and may be associated with progression of the tumor and treatment response. By applying the techniques of mass spectrometry we would like to assess the protein profile of exosomes released by melanoma cells and determine whether these changes correlate with selected clinical parameters. The model tests are exosomes released in vivo from melanoma cells (MMTEX). Proteins of exosomes were subjected to qualitative and quantitative analysis by LC-MS/MS. Proteins were digested by trypsin and were subsequently purified on C18 StageTips which significantly improves the chromatographic separation and allows identification of a higher number of proteins. In addition, after digestion the obtained peptides were fractionated and separated using ion chromatography and reversed-phase chromatography (C18 column), and then analysed by tandem mass spectrometry analysis. To evaluate protein content and verify the presence of exosomes we were used the Western blot technique or flow cytometry.

2021-08-12 | PXD021285 | Pride

Acetylation and phosphorylation changes to cardiac proteins in experimental HFpEF due to metabolic risk reveal targets for treatment

Project description:Aims: Despite the high prevalence of heart failure with preserved ejection fraction (HFpEF), the pathomechanisms remain elusive and specific therapy is lacking. Disease-causing factors include metabolic risk, notably obesity. However, proteomic changes in HFpEF are poorly understood, hampering therapeutic strategies. We sought to elucidate how metabolic syndrome affects cardiac protein expression, phosphorylation and acetylation in the Zucker diabetic fatty/Spontaneously hypertensive heart failure F1 (ZSF1) rat HFpEF model, and to evaluate some changes regarding their potential for treatment. Main methods: ZSF1 obese and lean rats were fed a Purina diet up to the onset of HFpEF in the obese animals. We quantified the proteome, phosphoproteome and acetylome of ZSF1 obese versus lean heart tissues by mass spectrometry and singled out targets for site-specific evaluation. Key findings: We found the acetylome of ZSF1 obese versus lean hearts more severely altered (21% of proteins changed) than the phosphoproteome (9%) or proteome (3%). Proteomic alterations, confirmed by immunoblotting, indicated low-grade systemic inflammation and endothelial remodeling in obese hearts, but low nitric oxide-dependent oxidative/nitrosative stress. Altered acetylation in ZSF1 obese hearts mainly affected pathways important for metabolism, energy production and mechanical function, including hypo-acetylation of mechanical proteins but hyper-acetylation of proteins regulating fatty acid metabolism. Hypo-acetylation and hypo-phosphorylation of elastic titin in ZSF1 obese hearts explained myocardial stiffening. Significance: Cardiometabolic syndrome alters posttranslational modifications, notably acetylation, in experimental HFpEF. Pathway changes implicate a HFpEF signature of low-grade inflammation, endothelial dysfunction, metabolic and mechanical impairment, and suggest titin stiffness and mitochondrial metabolism as promising therapeutic targets.

2022-10-12 | PXD036259 | Pride

BCL2L13 regulates sarcoplasmic reticulum-mitochondria calcium flux in skeletal muscle

Project description:The physical connection between mitochondria and endoplasmic or sarcoplasmic reticulum is an essential signaling hub to ensure organelle and cellular functions. In skeletal muscle, ER/SR-mitochondria calcium (Ca2+) signaling is crucial to maintain cellular homeostasis during physical activity. High expression of BCL2L13, a member of the BCL-2 family, was suggested as an adaptive response in endurance-trained human subjects. The aim of this study was to describe the molecular and physiological functions of BCL2L13. Using a zebrafish knockout model, we assessed the physiological changes, alterations of skeletal muscle structure, differences in the muscle proteome, and mitochondrial metabolism caused by the loss of Bcl2l13. We used cellular models to define the subcellular location and the mechanistic role of Bcl2l13. The loss of Bcl2l13 in zebrafish decreased swimming capacity and activity. Skeletal muscle fast fiber cross sectional area was reduced in knockout fish. Muscle proteome uncovered changes in protein turnover, transmembrane transport and expression of Ca2+ signaling proteins compared to wild type fish.

2024-07-25 | PXD044765 | Pride

Integrated omic analysis reveals multilevel control of renal and systemic metabolism by the renal tubular circadian clock

Project description:Circadian rhythmicity in renal function suggests a requirement for circadian adaptations in renal metabolism. We studied circadian changes in renal metabolic pathways using integrated transcriptomic, proteomic and metabolomic analysis performed on control mice and mice deficient in the circadian clock gene Bmal1 in the renal tubule (cKOt mice). Proteins were extracted from whole kidneys of 60 mice. Of these, 30 were conditional knockouts of Arntl (Bmal1) and 30 were of control genotype. They were housed under 12-hours light/12-hours dark cycles and were sacrificed at six different time points: zeitgeber time ZT 0, ZT 4, ZT 8, ZT 12, ZT 16, ZT 20 ( ZT 0 being the time of light on and ZT 12 the time of light off). Five replicates per genotype and time point were analysed.

2023-03-15 | PXD036803 | Pride

Molecular chaperone Hsp90 supports adaptive cell size increase in response to chronic stress

Project description:Hsf1, well known for its role in acute stress responses, is required for the cell size increase, and that the molecular chaperone Hsp90 is essential for coupling the cell size increase to augmented translation through a translational "rewiring stress response". We propose that this protective process of chronic stress adaptation contributes to the increase in size as cells get older, and that its failure promotes aging.

2023-12-01 | PXD039672 | Pride

Reanalysis of a proteome-wide level study with MaxLynx

Project description:Reanalysis of the publicly available proteome-wide level dataset with DSBU from Goetze et al., Anal Chem. 2019 (PXD012546).

2022-01-11 | PXD027188 | Pride

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

Project description:Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of characterization in microbes other than Escherichia coli. Here, we have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. We merged the annotated small proteome of Salmonella with new small proteins predicted with in silico and experimental approaches. We then exploited existing and newly generated global datasets that provide information on small open reading frame expression during infection of epithelial cells (dual RNA-seq), contribution to bacterial fitness inside macrophages (TraDIS), and potential engagement in molecular interactions (Grad-seq). This integrative approach suggested a new role for the small protein MgrB beyond its known function in regulating PhoQ. We demonstrated a virulence and motility defect of a Salmonella ΔmgrB mutant and revealed an effect of MgrB in regulating the Salmonella transcriptome and proteome under infection-relevant conditions. Overall, our study highlights the power of interpreting available “omics” datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.

2020-12-07 | PXD018754 | Pride

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