NRVM Conditioned Media Proteomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Rattus Norvegicus (rat)
TISSUE(S): Cell Culture, Electrically Active Cell
DISEASE(S): Cardiovascular System Disease
SUBMITTER: 
Stephanie Kereliuk
LAB HEAD: Walter J. Koch
PROVIDER: PXD050356 | Pride | 2024-04-22
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| checksum.txt | Txt | |||
| proteinGroups__KochW_18-G079_Rat.xlsx | Xlsx | |||
| proteinGroups__KochW_18-G079_RatRaw.xlsx | Xlsx |
Items per page: 5 1 - 3 of 3 |
Similar Datasets
Project description:analysis how HDAC inhibitior TSA increase cispkatin cytotoxicity
2024-06-23 | PXD052203 | Pride
Project description:WE TEST THE PROTEIN CHANGES WHEN A549 cells treated with DDP OR TSA.
2024-06-23 | PXD052305 | Pride
Project description:Pretreated human follicular fluid was prepared for targeted metabolomics experiments. For this purpose, 12-point standard calibration curves in the respective range with reference material were measured, and the limit of detection (LOD) and limit of quantification (LOQ) for each neurotransmitter under investigation were calculated. LC-MS/MS was conducted by an ultra-performance liquid chromatography method using a Waters ACQUITY UPLC BEH C18 column (2.1 mm×100 mm, 1.7 µm, Waters, USA). The Waters acquisition UPLC was coupled to an API 4000 triple quadrupole mass spectrometer (AB SCIEX, USA). The mobile phase A buffer was 10% methanol in water (containing 0.1% formic acid), and the mobile phase B buffer was 50% methanol in water (containing 0.1% formic acid). The LC gradient elution was at a flow rate of 0.3 mL/min at 0-8.0 min and 0.4 ml/min at 8.0-17.5 min, then 10%-30% B at 0-6.5 min; 30%-100% B at 6.5-7 min; 100% B at 7-14min; and 100%-10% B at 14-17.5min. The injection volume was 5 µl and the column temperature was set to 40 °C. Twenty-three metabolites (Ach: Acetylcholine chloride; Gln: Glutamine; Glu: Glutamate; His: L-Histidine; NE: norepinephrine; Tyr:Tyrosine; Trp:Tryptophan; Kyn: Kynurenine; GABA: 4-Aminobutyric acid;HisA:Histamine; PA:Picolinic acid;TyrA:Tyramine;DA:Hydroxytyramine hydrochloride; TrpA:Tryptamine;5-HT:Serotonin hydrochloride;E:Adrenaline hydrochloride;KynA:Kynurenic acid;5-HIAA:5-Hydroxyindole-3-acetic acid;DOPA:Levodopa;XA:Xanthurenic acid;VWA:Vanillymandelic Acid; 5-HTTP:5-Hydroxytryptophan;MT:Melatonine)were simultaneously reported in LC-MS/MS multiple reaction monitoring (MRM) mode. Data analysis was performed with Analyst 1.6 software.
2022-08-12 | PXD031560 | Pride
Project description:Cholangiocarcinomas (CCAs) are heterogeneous biliary cancers with dismal prognosis. Their etiologies remain mostly unclear, although primary sclerosing cholangitis (PSC) is a well-known risk factor. There is an urgent need of accurate non-invasive biomarkers for early CCA diagnosis and to predict patient´s prognosis, which may improve their clinical management and outcome. Here, by high-throughput proteomic analysis of serum extracellular vesicles (EVs), we identified diagnostic and/or prognostic biomarkers specific for CCAs in patients with PSC, and others common to all CCA subtypes. Bulk RNA tissue transcriptomic data revealed that these biomarkers are predominantly expressed in hepatobiliary tissues, being expressed in different liver cell types. Furthermore, single-cell RNAseq (scRNA-seq) analysis revealed that the expression of these biomarkers was preferentially found in malignant cholangiocytes within CCA tumors. In summary, these results highlight the potential of serum EVs to reflect cancer presence, especially for difficult-to-diagnose malignancies, including CCA."
2023-07-20 | PXD026197 | Pride
Project description:Addictive drugs including opioids activate signal transduction pathways that regulate gene expression in the brain. However, changes in CNS gene expression following morphine exposure are poorly understood. We studied the effect of short- and long-term morphine treatment on gene expression in the hypothalamus and pituitary using genome-wide DNA microarray and real-time reverse transcriptase polymerase chain reaction (RT-PCR) analyses. In the hypothalamus, we found that short-term morphine administration up-regulated (at least 2-fold) 39 genes and down-regulated six genes. Long-term morphine administration up-regulated 35 genes and down-regulated 51 hypothalamic genes. In the pituitary, we found that short-term morphine administration up-regulated (at least 2-fold) 110 genes and down-regulated 29 genes. Long-term morphine administration up-regulated 85 genes and down-regulated 37 pituitary genes. Strikingly, microarray analysis uncovered several genes involved in food intake (neuropeptide Y, agouti-related protein, and cocaine and amphetamine-regulated transcript) whose expression was strongly altered by morphine exposure in either the hypothalamus or pituitary. Subsequent RT-PCR analysis confirmed similar gene regulation of noteworthy genes in these regions. Finally, we found functional correlation between morphine-induced alterations in food intake and regulations of genes involved in this process. Changes in genes related to food intake may uncover new pathways related to some of the physiological effects of opioids. Keywords: Comparative treatment versus placebo 8 samples analyzed: 4 from hypothalamus (2 biological replicates and 2 dye swaps) and 4 from pituitary (2 biological replicates and 2 dye swaps) 8 samples analyzed: 4 from hypothalamus short term treatment (2 biological replicates and 2 dye swaps) and 4 hypothalamus long term treatment (2 biological replicates and 2 dye swaps)
2008-09-30 | E-GEOD-9525 | biostudies-arrayexpress
Project description:Organic acid secretion is a widespread physiological response of plants to alkalinity. However, the features of alkali-induced secretion of organic acid and the underlying mechanism are poorly understood. Herein, it was indicated that oxalate was the main organic acid synthesized and secreted in vine roots, and acetate synthesis and malate secretion were also promoted under NaHCO3 stress. NaHCO3 stress enhanced H+ efflux rate of vine roots, which was related to plasma membrane H+-ATPase activity. Transcriptomic profiling revealed that carbohydrate metabolism was the most significantly altered biological process under NaHCO3 stress; a total of seven genes related to organic acid metabolism were significantly altered, including two PEPCs and PEPCKs. Additionally, the expression levels of five ABC transporters, particularly ABCB19, as well as two malate transporter ALMT2s, were largely upregulated by NaHCO3 stress. Phosphoproteomic profiling demonstrated that the altered phosphoproteins were primarily related to binding, catalytic activity and transporter activity in light of their molecular functions. The phosphorylation levels of PEPC3, two plasma membrane H+-ATPases 4 and ABC transporters ABCB19 and PDR12 were significantly increased. Additionally, the inhibition of ethylene synthesis and perception completely blocked NaHCO3-induced organic acid secretion, while the inhibition of IAA synthesis reduced NaHCO3-induced organic acid secretion. Collectively, our results demonstrated oxalate as the main organic acid under alkali stress and the necessity of ethylene in mediating organic acid secretion, as well as further identified several candidate genes and phosphoproteins responsible for organic acid metabolism and secretion.
2019-11-11 | PXD013746 | Pride
Project description:The largest family of p97 cofactors is the UBXD protein family, whose members all carry an Ubiquitin Regulatory X (UBX) domain that enables binding to p97. We analysed one member of this family, the largely uncharacterised UBXD9 protein. To shed a light on the UBXD9 interactome, we used independent approaches to identify new interacting proteins. As a result, we confirmed p97 (also known as valosin-containing protein, VCP) as an interaction partner of UBXD9 and identified new interaction partners.
2021-08-26 | PXD027162 | Pride
Project description:The largest family of p97 cofactors is the UBXD protein family, whose members all carry an Ubiquitin Regulatory X (UBX) domain that enables binding to p97. We analysed one member of this family, the largely uncharacterised UBXD9 protein. To shed a light on the UBXD9 interactome, we used independent approaches to identify new interacting proteins. As a result, we confirmed p97 (also known as valosin-containing protein, VCP) as an interaction partner of UBXD9 and identified new interaction partners.
2021-08-26 | PXD027160 | Pride
Project description:The overall goal of the project is to identify candidate biomarkers of Active infection with Mycobacterium tuberculosis (Mtb) in individuals with or without HIV. Samples were analyzed from two tuberculosis (TB) endemic countries, Brazil and South Africa (SA), as well as from the United States (US). The US site included patients that were in the early stages of Active TB, with mean symptom duration of 1.5 months. The subjects from the Brazil site had mean symptom duration of 6 months, and the SA site subjects had advanced TB. All sites also provided samples asymptomatic for TB or with Latent TB infection. The US and SA sites also had subjects with and without HIV co-infection, whereas the Brazilian subjects were all HIV-. This specific dataset corresponds to the Discovery step of the study, for the US center.
2019-11-22 | PXD000517 | Pride
Project description:Abstract: ArtinM, a D-mannose-binding lectin from Artocarpus heterophyllus induces the activation of a Mast cell, neutrophils, macrophages, and CD4+ and CD8+ T cells, via carbohydrate recognition. we previously reported, that ArtinM is able to induce IL-17 and IL-12p40 production in murine B cells. Here, we further investigated the effects of ArtinM on murine B lymphocytes and Raji and Daudi cells, both human cell lines derived from non-Hodgkin lymphoma. We showed that ArtinM did not induce cell proliferation and low levels of IL-2, IFN-γ, and IL-12 were produced by murine B cells. However, high concentrations of ArtinM induced apoptosis of murine B cells. Then, evaluated the cytotoxic effect of ArtinM lectin against Raji and Daudi cells. we observed the ArtinM ability to reduce cell growth and cell viability, with a more pronounced cytotoxic effect on Raji cells. In addition, we observed the absence of DNA fragmentation, a strong indication of the exclusion of the apoptosis cascade via mitochondrial pathway, and the possible involvement of PTK, kinases of Src family, and CD45 phosphatase activity under Lck molecule in the cytotoxic effect of ArtinM in the Raji and Daudi cells. Thus, the present work demonstrates the limitations of the immunomodulatory effect of ArtinM under murine B cells, and provides insights in the investigative field in the non-Hodgkin lymphoma treatment, via carbohydrate recognition.
2023-03-11 | PXD029399 | Pride