Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic analysis of hippocampal tissue in mice in acute temporal lobe epilepsy

ABSTRACT: A total of 5762.0 proteins were identified in this study, of which 4891.0 proteins contained quantitative information. If a 1.2-fold differential expression change threshold is used and a statistical test t-test p-value < 0.05 is used as the significance threshold, then among the proteins quantified, we found that 95 proteins were up-regulated and 45 proteins were down-regulated in the treatvscontrol comparison group.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Brain

SUBMITTER: Cong Huang

LAB HEAD: Jiahang Sun

PROVIDER: PXD040967 | Pride | 2023-05-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Combined transcriptomics and proteomics forecast analysis for potential biomarker in the acute phase of temporal lobe epilepsy.

Huang Cong C You Zhipeng Z He Yijie Y Li Jiran J Liu Yang Y Peng Chunyan C Liu Zhixiong Z Liu Xingan X Sun Jiahang J

Frontiers in neuroscience 20230330

<h4>Background</h4>Temporal lobe epilepsy (TLE) is a common chronic episodic illness of the nervous system. However, the precise mechanisms of dysfunction and diagnostic biomarkers in the acute phase of TLE are uncertain and hard to diagnose. Thus, we intended to qualify potential biomarkers in the acute phase of TLE for clinical diagnostics and therapeutic purposes.<h4>Methods</h4>An intra-hippocampal injection of kainic acid was used to induce an epileptic model in mice. First, with a TMT/iTRA ...[more]

PMID: 37065920

Similar Datasets

Quantitative proteomic study of total protein TMT labeling in 18 pig liver samples

Project description:Based on the work flow of quantitative proteomic analysis combined with TMT labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS), this study carried out quantitative proteomic analysis on the liver tissues of Tibetan pigs and Yorkshire pigs in Shannan (about 4000 m), Linzhi (about 3000 m) and Jiuzhaigou (about 1500 m), and compared the differences of protein mass spectra between the liver of living pigs at three altitudes.

2023-03-11 | PXD039758 | Pride

Proteomics Reveals the Potential Mechanism of Tanshinone IIA Promoting the Ex Vivo Expansion of Human Bone Marrow Mesenchymal Stem Cells.

Project description:Bone marrow mesenchymal stem cells (BMSCs) is a promising cell type for tissue engineering, however, the application of BMSCs are largely hampered for the limited number harvested from bone marrow cells. The methods or strategies that focused on promoting the capacity of BMSCs expansion ex vivo become more and more important. Tanshinone IIA (Tan IIA), the main active components of Danshen, has been found to promote BMSCs proliferation, but the underlying mechanism is still unclear. This present work employed biological techniques combined with quantitative proteome analysis to explore the effect and underlying mechanism of Tan IIA on the ex vivo expansion capacity of BMSCs from human. The results showed that a total of 84 differentially expressed proteins were annotated and among them 51 upregulated proteins and 33 downregulated proteins were identified. Besides, Tan IIA could promote hBMSCs proliferation by regulating the progression of S phase via increasing the release of fibroblast growth factor 2 (FGF2), FGF-mediated PI3K/AKT signaling pathways may play an important role in Tan IIA’s effect on hBMSCs expansion. The results of this study may provide further evidence about the potential of Tan IIA to be used for the research of hBMSCs therapies.

2022-11-28 | PXD036093 | Pride

mice Renal tubular epithelial cells LC-MS/MS

Project description:Diabetic nephropathy is considered one of the most common microvascular complications of diabetes and the pathophysiology involves multiple factors. Progressive diabetic nephropathy is believed to be related to the structure and function of the tubular epithelial cells in the kidney. However, the role of lysine acetylation in lesions of the renal tubular epithelial cells arising from hyperglycemia is poorly understood. Consequently, in this study, we cultured mouse renal tubular epithelial cells in vitro under high glucose conditions and analyzed the acetylation levels of proteins by liquid chromatography-high-resolution mass spectrometry. We identified 48 upregulated proteins and downregulated 86 proteins. In addition, we identified 113 sites with higher acetylation levels and 374 sites with lower acetylation levels. Subcellular localization analysis showed that the majority of the acetylated proteins were located in the mitochondria (43.17%), nucleus (28.57%) and cytoplasm (16.19%). Enrichment analysis indicated that these acetylated proteins are primarily associated with oxidative phosphorylation, the citrate cycle (TCA cycle), metabolic pathways and carbon metabolism. In addition, we used the MCODE plug-in and the cytoHubba plug-in in Cytoscape software to analyze the PPI network and displayed the first four most compact MOCDEs and the top 10 hub genes from the differentially expressed proteins between global and acetylated proteomes. Finally, we extracted 37 conserved motifs from 4915 acetylated peptides. Collectively, this comprehensive analysis of the proteome reveals novel insights into the role of lysine acetylation in tubular epithelial cells and may make a valuable contribution towards the identification of the pathological mechanisms of diabetic nephropathy.

2022-02-17 | PXD029651 | Pride

lysine acetylation and succinylation in Streptomyces coelicolor

Project description:To determine the acetylome of S. coelicolor, the wild-type S. coelicolor sample was prepared with three biological replicates and two technical replicates and analyzed. To quantify the acetylome and succinylome, three samples (wild-type, ∆SccobB1, and ∆SccobB2) with three biological replicates were prepared and analyzed. The cells were harvested, digested, and then subjected to affinity enrichment before LC-MS/MS analysis.

2021-07-13 | PXD027205 | Pride

Bulk RNA-seq of MilliporeSigma SCC300 human iPSC-derived colon organoids compared with undifferentiated human iPSCs and MilliporeSigma SCC321 human patient-derived colon organoids

Project description:Experiment intended to obtain expression profiles of iPSC-derived human colon organoids compared to undifferentiated human iPSCs and a patient-derived colon organoid line

2021-10-25 | E-MTAB-11026 | biostudies-arrayexpress

LBP resists hepatic oxidative stress by regulating LD homeostasis

Project description:we explored the novel role of Lipopolysaccharide-binding protein (LBP) as an anti-oxidant, which can capture unsaturated triglyceride (TG) into LDs to avoid lipid peroxidation. Oxidative stress upregulates LBP level and promotes LDs growth via the LBP/TG phase transition. Upon N-Acetyl-L-cysteine (NAC) elimination of ROS, LBP is exported from LD along with PRDX4, resulting in an increase in phospholipid synthesis. Chronic stress causes LBP upregulation and leads to obesity, which can be rescued by NAC treatment in vivo. These results support that LBP maintains homeostasis by coupling lipid metabolism and redox signal, which provides insights into redox medicine that mitigate stress-induced metabolic dysfunction.

2024-04-10 | PXD040940 | Pride

Effect of ATP2 deletion on protein expression in Candida albicans

Project description:To investigate the effect of ATP2 knockdown on the protein expression of Candida albicans, we performed proteomic assays for atp2Δ/Δ and wild type strains. A total of 4000.0 proteins were identified in this study, of which 3652.0 proteins contained quantitative information. If a 1.5-fold differential expression change threshold and a statistical test t-test p-value < 0.05 were used as the significance threshold, then among the quantified proteins, we found that 112 proteins were up-regulated and 268 proteins were down-regulated in atp2Δ/Δ cells. Based on the above data, we performed systematic bioinformatics analysis (protein functional annotation) of all identified proteins, and performed functional classification, functional enrichment and functional enrichment-based clustering analysis of all differentially expressed proteins.

2021-09-10 | PXD024039 | Pride

Proteomics Analysis of the Mechanism of AMP-17 against Candida albicans

Project description:Candida albicans is the most common human fungal pathogen in immunocompromised individuals. With the emergence of clinical fungal resistance, there is an urgent demand to develop novel antifungal agents. The antibacterial peptide (AMP) is an important component in the innate immune system and has a good therapeutic effect on patients infected with microorganisms. AMP-17, a novel AMP from Musca domestica, has an antifungal effect against C. albicans, but the mechanism of antifungal action remains unclear. In this study, we performed proteomic analysis of C. albicans treated AMP-17 and No drug using a combination of a series of cutting-edge technologies, including TMT labeling, HPLC classification and quantitative proteomics based on mass spectrometry. A total of 3,931 proteins were identified, of which 3,600 contained quantitative information. With a 1.5-fold change threshold and a t-test p-value <0.05 as a standard, 423 differentially expressed proteins (DEPs) were up-regulated and 180 differentially expressed proteins (DEPs) were down-regulated in the quantitative AMP_17/con comparison group. In these DEPs, proteins associated with ergosterol biosynthesis, oxidative stress and cell wall were identified as significantly up-regulated, while proteins involved in fatty acid biosynthesis were identified as significantly down-regulated. In addition, using the KEGG enrichment assay, seven significant KEGG pathways were identified, primarily involved in oxidative phosphorylation, propionic acid metabolism, and fatty acid metabolism. These results showed that AMP-17 induces a complex organism response to C. albicans, indicating that AMP-17 can inhibit growth by affecting multiple targets in C. albicans cells.

2019-10-23 | PXD015469 | Pride

A cooperative organelle biogenesis program in mammalian cells

Project description:The compartmentalisation of distinct organelles within eukaryotic cells is essential for their diverse functions, however, how their structures and functions depend on each other has not been systematically explored. We combined a fluorescent reporter of mitochondrial stress with genome-wide CRISPR knockout screening and identified networks of genes involved in the biogenesis and metabolism of diverse organelles. Targeted organelle gene knockouts identified that defects in peroxisomes, Golgi, and ER cause mitochondrial fragmentation and dysfunction. Correlative light and electron microscopy analysed using artificial intelligence-directed voxel extraction revealed in unprecedented detail how impaired mitochondrial interactions with diverse organelles caused cell-wide defects in their morphology and biogenesis. Multi-omics analyses identified a unified proteome stress response and global shifts in lipid and glycoprotein homeostasis that are elicited when organelle biogenesis is compromised. Our comprehensive resource has defined metabolic and morphological interactions between organelles that can be mined to understand how changes in organelle components drive diverse cellular pathologies.

2023-10-04 | PXD033871 | Pride

Epitope mapping of potential novel immunogenic proteins of Campylobacter jejuni NCTC 11168

Project description:A number of seven proteins were selected during immunoscreening and further analyses. The proteins were in silico divided into overlapping 15-mer oligopeptides with an overlap of 11 residues. The microarrays were incubated with different antibodies to C. jejuni, Escherichia coli and Salmonella enterica. Each microarray was separated into three individual incubation chambers using ProPlate 3-Well modules. Within each incubation chamber, each peptide was spotted in triplicate with the controls spotted nine times each. The controls included human-IgG, rabbit-IgG, mouse-IgG and myelin basal protein (MBP). Each chamber was incubated independently using different polyclonal antibodies to C. jejuni, and for specificity testing, with an antibody to E. coli or S. enterica. Thus, samples 4_1, 4_2, 5_1 and 5_2 represent epitope mapping of three proteins with C. jejuni antibodies, while 6_1, 6_2, 7_1 and 7_2 represent the data after incubation with an E. coli antibody investigating unspecific interactions of the antibody to the potential linear epitopes from C. jejuni. Finally, for four different proteins from C. jejuni, the set two indicated by S2 was performed. Here, S2_6_1, S2_7_1, S2_7_2, S2_8_1 and S2_8_2 indicate epitope mapping after incubation with antibodies to C. jejuni, while the remaining samples were performed to test these latter 4 proteins for specificity by incubation with antibody to S. enterica.

2013-04-06 | E-GEOD-45542 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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