MRM (Multiple Reaction Monitoring) quantitation of the blood plasma and serum samples from healthy donors
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q TRAP
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Blood Plasma, Blood Serum
DISEASE(S): Disease Free
SUBMITTER: 
Georgij Arapidi
LAB HEAD: Georgij Pavlovich Arapidi
PROVIDER: PXD027793 | Pride | 2024-06-14
REPOSITORIES: Pride
Similar Datasets
Project description:Blood flow promotes emergence of definitive hematopoietic stem cells (HSCs) in the developing embryo, yet the signals generated by hemodynamic forces that influence hematopoietic potential remain poorly defined. In transplantation assays of hematopoietic reconstitution, we find that fluid shear stress endows long-term multilineage engraftment potential upon early hematopoietic tissues at E9.5 not previously described to harbor HSCs. Effects on hematopoiesis appear to be mediated in part by prostaglandin E2 (PGE2) and the cyclic AMP-protein kinase A (cAMP-PKA) signaling axis. Studies of Ncx1 cardiac mutants corroborate that blood flow is required for sufficient COX2 levels and phosphorylation of CREB. Further implicating PGE2 in mediating the effects of shear stress, we find that E10.5 and E11.5 AGM treated transiently with the synthetic analog dmPGE2 engraft more robustly and contribute to greater lymphoid reconstitution. These data provide a mechanism by which biomechanical forces induced by blood flow modulate hematopoietic potential. - AGM from C57BL/6J embryos at 10.5 days gestation (E10.5) were isolated by microdissection from uteri of pregnant dams, following by gentle dissociation by Accutase with agitation at room temperature for 20 minutes. Single cell suspension was seeded on microfluidic IBIDI VI^0.4 6-channel slides (0.8 to 1x10^7 cells per channel) and permitted to attach for 8 hours. Fluid movement was then applied to each channel using a Harvard Apparatus PHD ULTRA programmable syringe pump for manangement of M5300 Myelocult medium. Cells were exposed either to static/low flow (0.0001 dyne/cm^2) or wall shear stress (WSS) of 5 dyne/cm^2 for 6 hours or 36 hours. In addition, some cells were treated with 10 uM indomethacin (indo) to inhibit COX2 activity and PGE2 synthesis. Upon collection of cells with RLT lysis buffer (QIAGEN RNeasy kit), six channels of identical treatment were pooled to comprise a single sample. 24 samples total are included in this study. 12 samples were collected after 6 hours and 12 after 36 hours. In detail, samples included at 6 hours: 3 static, 3 static with indo, 3 WSS, 3 WSS with indo; and at 36 hours: 3 static, 3 static with indo, 3 WSS, 3 WSS with indo. Sample labels begin with the timepoint collected and end with the replicate number, i.e., 06WSS1 for the 6 hour collection of the first replicate of the WSS sample.
2015-04-05 | E-GEOD-62463 | biostudies-arrayexpress
Project description:Anopheline mosquitoes transmit Plasmodium parasites to humans, and are responsible for an estimated 219 million cases of malaria, leading to over 400,000 deaths annually. The mosquito’s immune system limits Plasmodium infection in several ways, and hemocytes, the insect white blood cells, are key players in these defense responses. However, the full functional diversity of mosquito hemocytes and their developmental trajectories have not been established. We use bulk RNA sequencing (scRNA-seq) to analyze the transcriptional profiles of hemocytes, of guts, and of carcasses of mosquito hemocytes in response to blood feeding or infection with Plasmodium. Data from three independent biological replicates for each condition and time-point (day 0, 1, 2, 3, and 7 after sugar-feeding, blood-feeding or P. berghei infection).
2020-08-27 | E-MTAB-9241 | biostudies-arrayexpress
Project description:Conventional in vitro cell cultures are relatively available and have been widely used in explaining many mechanisms, but their simple construction is not directly applied to the in vivo environment. A possible solution to overcome this problem is special in vitro model maintained with cardiac slices. Slices show a preserved architecture, multi-cellularity and physiology of the heart tissue. This approach creates a bridge between the gap in cellular and in vivo studies. This study demonstrated that it is possible to find protein biomarkers between rat myocardial slices which were stretched to sarcomere lengths (SL) within the physiological range of 1.8–2.4μm and slices cultured without electromechanical stimulation and with fresh myocardial slices.
2022-08-25 | PXD034891 | Pride
Project description:The study concerns untargeted metabolomics in gastric and colorectal cancer patients. It was analyzed using mass spectrometry.
2024-05-01 | PXD051921 | Pride
Project description:Clostridium ljungdahlii derives energy by acetogenesis as a lithotrophic pathway and as part of various organotrophic pathways. Its recently sequenced genome has made it possible to discover changes in gene expression that occur in different growth modes, from which strategies for biofuel production may be developed. C. ljungdahlii was grown with fructose as an organoheterotrophic substrate and also lithoautotrophically, either on syngas or with H2 as the electron donor and CO2 as the electron acceptor. RNA extracted from all three conditions was analyzed by hybridization to a microarray, and gene expression was compared quantitatively by RNA-Seq of C. ljungdahlii grown with fructose and with H2 and CO2. Results. Strongly upregulated (> 10-fold, p < 0.05) genes with both syngas and H2/CO2 encode enzymes that degrade aspartate and arginine through the urea cycle to control the release of ammonia from amino acids. Numerous genes for uptake and degradation of peptides and amino acids, response to sulfur starvation, and molybdopterin-dependent pathways were also significantly (> 2-fold, p < 0.05) upregulated, along with three potentially NADPH-producing pathways for which the key metabolites are (S)-malate, ornithine and 6-phospho-D-gluconate. Upregulation of genes implicated in quorum sensing, sporulation and cell wall remodeling suggests a global and multicellular response to lithoautotrophic conditions. With syngas, (R)-lactate dehydrogenase and associated electron transfer flavoproteins were upregulated, representing a route of electron transfer from ferredoxin to NAD that is independent of the proton-translocating Rnf complex. With H2/CO2, a flavodoxin and histidine biosynthesis enzymes were upregulated. Genes for degradation of purine bases entering the cell by facilitated diffusion were upregulated in lithotrophic cells, whereas genes for degradation of adenine or adenosine derivatives entering by active transport were significantly (2-fold, p < 0.05) downregulated. The most downregulated genes, after those specific to fructose metabolism, encode enzymes of pyrimidine and purine biosynthesis, arginine fermentation to ornithine, threonine biosynthesis and phosphate uptake. Genes for biogenesis of an intracytoplasmic microcompartment were downregulated, within which (S)-1,2-propanediol dehydratase and other enzymes may dispose of methylglyoxal, a toxic byproduct of glycolysis, as 1-propanol. Several redox-active proteins, both cytoplasmic and membrane-associated, and predicted cell surface proteins were identified as differentially regulated. Conclusion. The transcriptomic profiles of C. ljungdahlii in lithoautotrophic and organoheterotrophic growth modes indicate large-scale physiological and metabolic differences, observations that may guide the production of biofuels and commodity chemicals with this species.
2017-06-01 | E-MTAB-3806 | biostudies-arrayexpress
Project description:Identify potential interactors of TRPC5OS in breast cancer cells.
2022-06-09 | PXD029020 | Pride
Project description:Aims: To investigate the inactivation kinetics of Bacillus cereus vegetative cells upon exposure to low-temperature nitrogen gas plasma and to reveal the mode of inactivation by transcriptome profiling. Methods and results: Exponentially growing B. cereus cells were filtered and put on agar plates. The plates, carrying the filters with the vegetative cells, were placed into nitrogen gas plasma at atmospheric pressure and cold temperature (~37°C). After different exposure times the cells were harvested for RNA extraction and enumeration. The RNA was used to perform whole transcriptome profiling using DNA microarrays. The transcriptome profile showed a large overlap with profiles obtained from conditions generating reactive oxygen species inside B. cereus. However, excess radicals such as peroxynitrite, hydroxyl and or superoxide were not found. Conclusions: Antibacterial activity of nitrogen gas plasmas is not based on UV radiation but on the formation of reactive oxygen or nitrogen species in the plasma jet rather than inside the targeted cells. Significance and impact of the study: This study represents the first investigation of differential gene expression on a genome-wide scale in B. cereus following nitrogen gas plasma exposure. This study may help to design cheap, safe, and effective plasma decontamination devices. Plasma treated sampes compared with nitrogen gas flow treated samples and plasma treated samples compared to untreated control samples. Nitrogen flow samples in duplicate, plasma treated samples 4 replicates. Replicates hybridized with dyes swapped.
2013-05-06 | E-GEOD-35060 | biostudies-arrayexpress
Project description:In this project we cloned 141 mammalian RhoGAPs/GEFs (112 human, 26 mouse, 2 rat, 1 chimpanzee) and performed a systematic study of their interactome, localisation and specificity. Here we submit the mass spectrometry data from the interactome screen.
2020-01-21 | PXD010144 | Pride
Project description:The inflammatory response after spinal cord injury (SCI) is an important contributor to secondary damage. Infiltrating macrophages can acquire a spectrum of activation states, however, the microenvironment at the SCI site favors macrophage polarization into a pro-inflammatory phenotype, which is one of the reasons why macrophage transplantation has failed. In this study, we investigated the therapeutic potential of the macrophage secretome for SCI recovery. We investigated the effect of the secretome in vitro using peripheral and CNS-derived neurons and human neural stem cells. Moreover, we perform a pre-clinical trial using a SCI compression mice model and analyzed the recovery of motor, sensory and autonomic functions. Instead of transplanting the cells, we injected the paracrine factors and extracellular vesicles that they secrete, avoiding the loss of the phenotype of the transplanted cells due to local environmental cues. We demonstrated that different macrophage phenotypes have a distinct effect on neuronal growth and survival, namely, the alternative activation with IL-10 and TGF-β1 (M(IL-10+TGF-β1)) promotes significant axonal regeneration. We also observed that systemic injection of soluble factors and extracellular vesicles derived from M(IL-10+TGF-β1) macrophages promotes significant functional recovery after compressive SCI and leads to higher survival of spinal cord neurons. Additionally, the M(IL-10+TGF-β1) secretome supported the recovery of bladder function and decreased microglial activation, astrogliosis and fibrotic scar in the spinal cord. Proteomic analysis of the M(IL-10+TGF-β1)-derived secretome identified clusters of proteins involved in axon extension, dendritic spine maintenance, cell polarity establishment, and regulation of astrocytic activation. Overall, our results demonstrated that macrophages-derived soluble factors and extracellular vesicles might be a promising therapy for SCI with possible clinical applications.
2024-02-14 | PXD048453 | Pride
Project description:Autophagy defects are a risk factor for Inflammatory Bowel Diseases (IBD) through unknown mechanisms. Whole-body conditional deletion of essential autophagy gene (ATG) Atg7 in adult mice (Atg7Δ/Δ) causes tissue damage and death within three months due to neurodegeneration without substantial effect on intestine. In contrast, we report here that whole-body conditional Atg5 deletion in adult mice (Atg5Δ/Δ) caused death within five days due to rapid autophagy inhibition, elimination of ileum stem cells, and loss of barrier function. Atg5Δ/Δ mice lost PDGFRα+ mesenchymal cells (PMCs) and Wnt signaling essential for stem cell renewal, which were partially rescued by exogenous Wnt. To assess the metabolic consequences of ATG5 loss in PMCs and the ileum, we performed Matrix-assisted laser desorption ionization (MALDI) coupled to imaging mass spectrometry (IMS) (MALDI-IMS) to distinguish between a specific metabolic defect in PMCs and an effect on the entire ileum.
2022-05-26 | PXD023428 | Pride