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Proteomicsproteome analysis using mass spectrometry (MS) in acute shYthdf2-mediated knockdown of cultured RGCs
To identify mouse retinal proteomics changes after Ythdf2 knockdown, we extracted the proteomics of E15.5 retina neurons which were cultured and infected with lentiviral shYthdf2 or shCtrl by urea. After using 100 mM TEAB (Sigma) to dilute the urea concentration to less than 2 M in each sample, trypsin...
ORGANISM(S): Mus Musculus (mouse) 
2022-04-04 | PXD017775 | Pride
Mouse  retina  ythdf2  knockdown knockdown Mouse retina ythdf2 
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ProteomicsDeep serum proteomics detects sex-influenced signature in a murine model of Alzheimer's disease
Alzheimer’s disease (AD) is the most common neurodegenerative disorder and is categorized by the deposition of extracellular amyloid plaques and intracellular neurofibrillary tangles. By using...
...te. Differential expression (DE) analysis between WT and 5xFAD mouse models showed essentially no protein changes except Lcn11. Interesting, our method detected 65 sex-dependent DE proteins with statistical significance (FDR < 0.05), including some earlier reported molecules related towards AD disease progression Serpina3h, Serpina3c, A1bg, Ncam2, Fgl1, Hamp, Kif15, Man2b2, Egfr, Prl etc, had adequate sensitivity and reproducibility to detect sex-dependent differentially expressed proteins in disease-related pathways. Hence, our newly developed protocol revealed alterations in key sex-related proteins that can be differentiated in serum analysis, both known and novel, which may be relevant to the development of assays for th...
ORGANISM(S): Mus Musculus (mouse) 
2024-05-21 | PXD044306 | Pride
Plasma Biomarker Alzheimer’s disease Tandem mass tag Proteomics Serum Proteome Mass spectrometry 
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ProteomicsClathrin IP_mouse sciatic nerve axons_Roylab_UCSD
...estion, lysate was subjected to incubation with beads conjugated with either clathrin heavy chain antibody or control IgG antibody for clathrin immunoprecipitation. MudPIT analysis was subsequently performed to identify proteins co-precipitating with clathrin.
ORGANISM(S): Mus Musculus (mouse) 
2021-08-12 | PXD027857 | Pride
Axons Clathrin Sciatic nerves 
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ProteomicsClpP protease modulates bacterial growth, stress response and bacterial virulence in Brucella abortus
Intracellular proteolysis via ATP-dependent proteases is a conserved biological process. The ATP-dependent C...
...y metabolites biosynthesis, transport and catabolism. Overall, our study revealed preliminary molecular mechanism between Clp protease, bacterial growth, stress response and bacterial virulence in Brucella strains
ORGANISM(S): Brucella Abortus (strain 2308) 
2023-10-24 | PXD034842 | Pride
Virulence Brucella Itraq analysis Clpp protease 
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Genomics,MultiomicsNational Institute of General Medical Sciences (NIGMS) Human Genetic Cell Repository Human Variation Panels including 100 African-Americans (HD100AA), 100 Caucasians (HD100CAU), 100 Han People of Los Angeles (HD100CHI) and 100 Mexican American Community of Los Angeles (HD100MEX)
<p>The Human Genetic Cell Repository is sponsored by the ...jected to rigorous quality control. The Repository was established in 1972 at Coriell and contains more than 9,500 cell lines, primarily fibroblasts and transformed lymphoblasts. The Repository has a major emphasis on inherited diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes s...
phs000211.v1.p1 | EGA
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ProteomicsDeep Multilayer Tissue Proteomics Identifies Molecular Networks in Alzheimer’s Disease Progression, human data
The molecular networks underlying Alzheimer’s disease (AD) are not well-defined. We present temporal profiling of >14,000 proteins and >34,000 phosphosites at the asymptomatic and symptomatic stages of AD, deep proteomics analysis of transgenic mouse models.
ORGANISM(S): Homo Sapiens (human) 
2019-11-11 | PXD007985 | Pride
systems biology netrin disease network Alzheimer’s disease proteomics transcriptome tau Alzheimer’s disease  mass spectrometry  proteomics  proteome  phosphoproteome  transcriptome  rna-seq  genomics  genome  systems biology  disease network  aβ  tau  netrin proteome phosphoproteome genome aβ mass spectrometry genomics rna-seq 
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ProteomicsIntegrated proteomics reveals autophagy degradation landscape in neurons and receptors regulating neuronal activity
Autophagy is a constitutive process of lysosomal degradation required for maintaining the homeosta...
...ys and organelles. Our study reveals the landscape of autophagy degradation in neurons and insight into mechanisms of neurological disorders linked to autophagy deficiency.
ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse) 
2024-06-22 | PXD048730 | Pride
Neuron Integrated proteomics Autophagy degradation Tandem mass tag Lc-ms/ms Mass spectrometry 
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ProteomicsTime-series proteome profiling analysis of the atria in a murine model of angiotensin II-induced atrial fibrillation
Atrial fibrillation (AF) is the most common form of arrhythmia observed in clinical cardiac diseases. Angiotensin II (Ang II) and elevation of blood pressure have been considered to be the main risk regulators of AF. However, the time series p...
...omatography coupled with tandem mass spectrometry (LC-MS/MS) technologies. This study defined the dynamic changes of the differentially expressed proteins (DEPs) involved in Ang II-induced AF, and identified that mitochondrial oxidative phosphorylation may play a key role in this disease. These findings provide a resource for understanding t...
ORGANISM(S): Mus Musculus (mouse) 
2022-04-04 | PXD022238 | Pride
Proteomics  time series protein expression profiling  angiotensin ii  atrial fibrillation atrial fibrillation time series protein expression profiling angiotensin ii Proteomics 
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ProteomicsQuantitative proteomic analysis reveals molecular adaptations in the hippocampal synaptic active zone of chronic mild stress-unsusceptible rats
Background: While stressful events are recognized as an important cause of major depressive disorder (MDD), some individuals exposed to life stressors maintain normal psychological functioning. Although the molecular mechanism(s) underlying this phenomenon remain unclear, abnormal transmission and plas...
ORGANISM(S): Rattus Norvegicus (rat) 
2015-11-05 | PXD002540 | Pride
Lc-ms/ms Triple tof 5600 Rat hippocampus Itraq 
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MetabolomicsUntargeted plasma metabolome identifies biomarkers in patients with extracranial arteriovenous malformations
<p>OBJECTIVE: This study aimed to investigate the plasma metabolic profile of ...
...acid, piperettine, 20-hydroxy-PGF2a, 2,2,4,4-tetramethyl-6-(1-oxobutyl)-1,3,5-cyclohexanetrione, DL-tryptophan, 9-oxoODE, alpha-Linolenic acid and dihydrojasmonic acid.

CONCLUSION: Patients with extracranial AVMs exhibited significantly altered metabolic patterns compared to healthy controls, which could be identified using plasma metabolomics. These findings suggest that metabolomic profiling can aid in the understanding of AVM pathophysiology and potentially inform clinical diagnosis and treatment.

1970-01-01 | MTBLS7753 | MetaboLights
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