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257 results for “Proteomic analysis”
The Role of Proteomics Analysis in Carcinogenesis in a Rat Mammary Cancer Model Induced by DMBA (7,12-dimethylbenz(α)anthracene)
<p>The dataset consists of raw data on protein concentration from a Nanodrop Spectrophotometer and raw data on protein molecular weight from SDS-PAGE</p>
Proteomics analysis for: The platelet transcriptome and proteome in Alzheimer's disease and aging: an exploratory cross-sectional study
<p>Alzheimer’s disease (AD) and aging are associated with platelet hyperactivity. However, the mechanisms underlying abnormal platelet function in AD and aging are yet poorly understood. To explore the molecular profile of AD and aged platelets, we investigated platelet activation (i.e., CD62P expression), proteome and transcriptome in AD patients, non-demented elderly, and young individuals as controls. AD, aged and young individuals showed similar levels of platelet activation based on CD62P expression. However, AD and aged individuals had a proteomic signature suggestive of increased platelet activation compared with young controls. Transcriptomic profiling suggested the dysregulation proteolytic machinery involved in the regulation of platelet function, particularly in the ubiquitin-proteasome system in AD and autophagy in aging. The functional implication of these transcriptomic alterations remains unclear and requires further investigations. </p>
Code. Midlife proteome-wide analysis identifies plasma biomarkers for 25-year dementia risk linked to diverse pathophysiology
<p>The code used for the analyses for the paper entitled "Midlife proteome-wide analysis identifies plasma biomarkers for 25-year dementia risk linked to diverse pathophysiology". </p>
Analysis of the proteomic profile in serum of irradiated nonhuman primates treated with Ex-Rad, a radiation medical countermeasure
<p>There are currently four radiation medical countermeasures that have been approved by the United States Food and Drug Administration to mitigate hematopoietic acute radiation syndrome, all of which are repurposed radiomitigators. The evaluation of additional candidate drugs that may also be helpful for use during a radiological/nuclear emergency is ongoing. A chlorobenzyl sulfone derivative (organosulfur compound) known as Ex-Rad, or ON01210, is one such candidate medical countermeasure, being a novel, small-molecule kinase inhibitor that has demonstrated efficacy in the murine model. In this study, nonhuman primates exposed to ionizing radiation were subsequently administered Ex-Rad as two treatment schedules (Ex-Rad I administered 24 and 36 h post-irradiation, and Ex-Rad II administered 48 and 60 h post-irradiation) and the proteomic profiles of serum using a global molecular profiling approach were assessed. We observed that administration of Ex-Rad post-irradiation is capable of mitigating radiation-induced perturbations in protein abundance, particularly in restoring protein homeostasis and immune response and mitigating hematopoietic damage, at least in part after acute exposure. Taken together, restoration of functionally significant pathway perturbations may serve to protect damage to vital organs and provide long-term survival benefits to the afflicted population.</p>
High though-put proteomics analysis of dental plaque cultured on Ti40Zr10Cu36Pd14 bulk metallic glass and Ti6Al4V surface
<p>High though-put proteomics analysis of dental plaque cultured on Ti40Zr10Cu36Pd14 bulk metallic glass and Ti6Al4V surface</p>
Serum proteomic analysis of sex differences during an acute low back pain episode
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Analysis of the proteomic profile in serum of irradiated nonhuman primates treated with Ex-Rad, a radiation medical countermeasure
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Data for: Getting over it? A proteomic analysis of mechanisms driving multigenerational acclimation to organic ultraviolet filters in Daphnia magna
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Proteomic analysis of serum markers in patients maintained on Antipsychotics
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Proteomics and phosphoproteomics analysis of the tyrosine phosphatase SHP2 acquired resistance to SHP099 in the context of AML
<p>Proteomics analysis of AML cell lines (MV-4-11, MOLM-13, EOL-1 and OCI-M1) presenting acquired resistance to SHP099 and their parent sensitive cells in presence of the SHP2 allosteric inhibitor SHP099 or DMSO (control). These samples were labelled with TMT and analysed by mass spectrometry. </p> <p>The same approach was conducted to analyse the phosphoproteome of MV-4-11 cells (parent and resistant) upon SHP099 treatment.</p> <p>These data are associated with the manuscript "<strong>Tyr-62 phosphorylation of the tyrosine phosphatase SHP2 enables acquired resistance to SHP2 allosteric inhibitors</strong>"</p>
Data from: Proteomic analysis of barley mapping population subjected to drought identifies proteins with genotype×environment interaction and pQTLs
Drought is one of the major abiotic stresses negatively influencing crop yield and is a serious issue in modern agriculture. To achieve further substantial crop improvements in terms of drought resistance it is necessary to incorporate scientific results into breeding strategies. However, most of the data on plant drought responses arises mostly from small-scale studies and, therefore, its use in breeding programs is very limited. Here, we present the results of the large-scale proteomic analysis performed on barley recombinant inbred lines (RILs) and their parental genotypes subjected to drought, applied shortly before tillering. The conducted proteomic analyses enabled us to monitor drought-induced proteome changes in leaf and root tissue, and to identify proteins that responded to drought in a genotype-specific manner, for instance Rubisco activase, luminal binding protein, phosphoglycerate mutase, glutathione S-transferase, heat shock proteins as well as enzymes involved in phenylpropanoid biosynthesis. We also demonstrated feasibility of incorporating proteomic data resulting from large-scale study into genetic linkage analysis, which constitutes a fundament in biotechnology-driven breeding strategies.
Data from: Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets
Background: Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets. Results: The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control. Conclusion: The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response. The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.
Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics - Data Supplement
<p>This the is Data Supplement for the article "Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics" submitted to the Journal of Proteomics 2015.</p>
R-code for: A systems level analysis of epileptogenesis-associated proteome alterations
<p>Despite intense research efforts, the knowledge about the mechanisms of epileptogenesis and epilepsy is still considered incomplete and limited. However, an in-depth understanding of molecular pathophysiological processes is crucial for the rational selection of innovative biomarkers and target candidates.</p> <p>Here, we subjected proteomic data from different phases of a chronic rat epileptogenesis model to a comprehensive systems level analysis. Weighted Gene Co-expression Network analysis identified several modules of interconnected protein groups reflecting distinct molecular aspects of epileptogenesis in the hippocampus and the parahippocampal cortex. Characterization of these modules did not only further validate the data but also revealed regulation of molecular processes not described previously in the context of epilepsy development. The data sets also provide valuable information about temporal patterns, which should be taken into account for development of preventive strategies in particular when it comes to multi-targeting network pharmacology approaches.</p> <p>In addition, principal component analysis suggests candidate biomarkers, which might inform the design of novel molecular imaging approaches aiming to predict epileptogenesis during different phases or confirm epilepsy manifestation. Further studies are necessary to distinguish between molecular alterations, which correlate with epileptogenesis versus those reflecting a mere consequence of the status epilepticus.</p>
Proteomics_Analysis for Maier et al. 2017
<p>This is an annotated proteomics data set used in the the paper "Impact of dietary resistant starch on the human gut microbiome, metaproteome and metabolome." mBio01343-17 </p> <p>Proteomics analysis was lead by Lang Ho Lee. Colin J. Brislawn is the informatics point-of-contact.</p> <p> </p>
Comparative membrane proteomic analysis of Tritrichomonas foetus isolates (non filtered Data Sets)
<p>Tritrichomonas foetus is a flagellated and anaerobic parasite able to infect cattle and felines. Despite its prevalence, there is no effective standardized or legal treatment for T. foetus-infected cattle; the vaccination still has limited success in mitigating infections and reducing abortion risk; and nowadays, the diagnosis of T. foetus presents important limitations in terms of sensitivity and specificity in bovines. Here, we characterize the plasma membrane proteome of T. foetus and identify proteins that are represented in different isolates of this protozoan. Raw proteomics data sets from MALDI-TOF Mass Spectrometry presented here corresponds to six T. foetus isolates (Tf0-Tf5). For Tf2 isolate also five membrane fractions are presented (f1-f5). </p>
Supplemntary tables S1-S6 related with the article entitled: LC-MS-Based Plasma Proteome Analysis in Nursery Pigs Fed Diets Enriched with Native Chicory Inulin
<p><span>Table S1: Composition of the pig diet: control diet (C) and diets supplemented with 1% (T1) or 3% (T2) of native chicory inulin.; Table S2: Nutrient contents of the control diet (C) and the diets supplemented with 1% (T1) or 3% (T2) of native chicory inulin.; Table S3: Chemical composition (%) of inulin (IN) used as a feed supplement.; Table S4: Porcine plasma proteins submitted for further analysis.; Table S5: Proteins significantly altered in response to the T1 diet.; Table S6: Proteins significantly altered in response to the T2 diet.</span></p>
Data for SWATH-based Quantitative Proteomic Analysis of Morus alba L. Leaf under Ultraviolet-B radiation and Dark Treatment
<p><em>Morus alba (M. alba) </em>have been used in traditional Chinese medicine. Since, previous studies indicated that the accumulation of several secondary metabolites was significantly induced by UV-B radiation with dark treatment. To investigate the response of <em>Morus alba</em> leaf to UV-B radiation and UV-B radiation followed by dark incubation (UVD), SWATH-based quantitative proteomic analysis was performed on <em>Morus alba</em> leaf of control, UV-B radiation and UV-B radiation then dark incubation. A total of 716 proteins were identified and quantified.</p>
Supplementary dataset for cell-free supernatant proteome analysis from Bacillus subtilis and Lactobacillus helveticus in response to pH changes
<p>Data obtained through Scaffold 5 was used for quantification of the proteins based on spectra count values. These spectral count values were normalized, and analysis of variance (ANOVA) performed to detect differential abundance among the treatments at the 95 % confidence level (p < 0.05).<br> </p>
Quantitative Proteome-wide O-Glycoproteomics Analysis with FragPipe
<p>Processed search results and parameter files supporting the analyses presented in the publication "Quantitative Proteome-wide O-Glycoproteomics Analysis with FragPipe".</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.