Eda67111-8258-44c3-bd88-dedf34c2b030 - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009067 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The cohort (n=53) consists of prostate cancer patients from Australia. For each patient, a pair of blood and tumour samples were collected. The sequencing data was mapped to hg38 reference. Blood BAMs are named with “-B†as suffix and tumour BAMs are named with “-T†as suffix.
| EGAD00001009066 | EGA
Project description:Propolis is a resinous honeybee product, rich in polyphenolic compounds and with high economic value. Although extensive studies regarding the chemical composition of different propolis extracts have been carried out, the propolis proteome remained unknown. The present study aimed at characterizing the proteome of two geographically-distinct propolis originating from Belgium and Iran. Propolis extracts were analysed by SDS-PAGE followed by MALDI-TOFand LC/ESI- mass spectrometry (MS). Our in-depth proteomic analysis led to the identification of honeybee venom and royal jelly proteins, and numerous plant-defense proteins in propolis, extending our understanding on the antimicrobial properties of this complex natural substance. The proteome of both propolis was mainly made up of proteins belonging to the poplar tree. The poplar PR-2 (β-1,3-glucanases) and PR-8 (acidic endochitinases) proteins were found to be the major components of both propolis extracts, while bee venom (Api m 1) and royal jelly allergens (MJRP 1and 2) were only identified in the propolis from Belgium. Overall, our proteome analyses revealed that propolis extracts from Belgium and Iran shared a core protein composition originating from the poplar proteome. The majority of identified proteins are involved in the plant defense against pathogens, some belonging to well-known pathogenesis-related families.
2026-03-26 | PXD039653 | Pride
Project description:Filamentous algae (FA) have potential advantages over microalgae for wastewater treatment. However, their implementation at large-scale is hindered by an inability to predict performance. This study compared the cellular responses (photosynthesis and respiration) and composition (pigments and photosystem proteins) of FA Oedogonium acclimatised to average summer and winter conditions (Melbourne, Australia). After 7 days of acclimation the Chl a content of summer acclimated (SA) algae was about half that of the winter acclimated (WA) algae, which can be related to a strategy to reduce photodamage under high light intensities. No statistically significant changes were observed in any identified proteins associated with photosystem PSII and the reaction centre of PSI. Transmission electron microscopy images revealed more prominent lipid bodies within the SA filaments than in WA filaments, but no discernible difference in the abundance of starch granules. Photosynthetic irradiance curves were compared for the SA and WA algae. Consistent with the differences in chlorophyll, the specific gross photosynthetic rate (µP, gross) was generally higher for the WA algae. The relative difference increased from around 2-fold at 15°C to 3-fold at 25°C, and then decreased to less than 1.5-fold at 30 °C and 35 °C. At all the tested temperatures, saturation irradiance levels were in the range of 75 – 500 µmol/m2·s. Photoinhibition was observed at 30 °C (above ~300 µmol/m2·s) and was more severe at 35 °C (above ~500 µmol/m2·s), with WA algae showing greater inhibition. In contrast, the respiration response was similar for the SA and WA algae. The study emphasises the significance of accounting for seasonal variations and their effects on biomass productivity and utilisation. The data obtained will enable the incorporation of acclimation and its effect on biochemistry and photosynthetic response into predictive models of FA performance in outdoor cultures.
2026-01-12 | PXD040798 | Pride
Project description:The inflammatory functions of the cytokine tumor necrosis factor (TNF) rely on its ability to induce cytokine production and to induce cell death. Caspase dependent and independent pathways – apoptosis and necroptosis – respectively, regulate immunogenicity by the release of distinct sets of cellular proteins. To obtain an unbiased, systems-level understanding of this important process, we here applied mass spectrometry-based proteomics to dissect protein release during apoptosis and necroptosis. We report hundreds of proteins released from human myeloid cells in time-course experiments. Both cell death types induce receptor shedding, but only apoptotic cells released nucleosome components. Conversely, necroptotic cells release lysosomal components by activating lysosomal exocytosis at early stages of necroptosis- induced membrane permeabilisation and show reduced release of conventionally secreted cytokines.
2020-07-18 | PXD014966 | Pride
Project description:Nocturnal home hemodialysis (NHD) [5 â 6 times a week, 6-8 hours per session] augments uremia clearance and is associated with an increase in hemoglobin level. We have used microarray to have a global image of the changes at the gene expression. Experiment Overall Design: Sixteen stable end-stage renal disease patients (age: 47 ñ 2 years; 9M) [mean ñ SEM] were studied. Total RNA (TRNA) was isolated from whole blood before and after 3 months of established NHD. Gene expression before and after NHD was acquired through hybridizations on Human HG-U133_PLUS2 GeneChip and genes with differential gene expression were identified.
2009-01-13 | E-GEOD-11227 | biostudies-arrayexpress
Project description:Spatial tissue proteomics integrating whole-slide imaging, laser microdissection and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONE® robotic system, which has the capacity to process 192 samples in three hours. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking and tryptic digest of low-input archival tissue samples. The seamless integration with the Evosep ONE LC system by centrifugation allows ‘on-the-fly’ sample clean-up, particularly pertinent for laser microdissected workflows. We validate our method in human tonsil archival tissue, where we profile proteomes of spatially-defined B-cell, T-cell and epithelial microregions of 4,000 µm2 to a depth of ~2,000 proteins and with high cell type specificity. We finally provide detailed equipment templates and experimental guidelines for broad accessibility.
2024-03-22 | PXD047762 | Pride
Project description:Mucopolysaccharidosis IIIB (MPS IIIB) is an inherited metabolic disease due to deficiency of α-N-Acetylglucosaminidase (NAGLU) enzyme with subsequent storage of undegradedheparan sulfate (HS). The main clinical manifestations of the disease are profound intellectual disability and neurodegeneration. To identify potential biomarkers and novel neuropathological mechanisms of MPS IIIB, a label-free quantitative proteomic approach was applied to compare the proteome profile of brains from MPS IIIB and control mice. Proteins were identified through a bottom up analysis and 130 were significantly under-represented and 74 over-represented in MPS IIIB mouse brains compared to wild type (WT). Multiple bioinformatic analyses of the differentially abundant proteins allowed to define three major clusters: proteins involved in cytoskeletal regulation, synaptic vesicle trafficking, and energy metabolism. The results highlight the involvement of these clustered proteins in the neuropathology of MPS IIIB disease. The proteins identified in this study would provide potential targets for diagnostic and therapeutic studies of MPS IIIB.
2020-02-26 | PXD017363 | Pride
Project description:This study involved the collection of 25 (16 female and nine male adults) plasma samples from bariatric surgery patients. Plasma was prepared from blood samples taken pre-surgery (within 48 hours, files with the suffix ‘Pre’) and nine months post-surgery (files with the suffix ‘Post’).
2025-03-17 | PXD057848 | Pride
Project description:In the marine environment, surface-associated bacteria often produce an array of antimicrobial secondary metabolites (MSMs), which have predominantly been perceived as competition molecules. However, they may also affect other hallmarks of surface-associated living, such as motility and biofilm formation. Here, we investigate the ecological significance of an antibiotic secondary metabolite, tropodithietic acid (TDA), in the producing bacterium, Phaeobacter piscinae S26. We constructed a markerless in-frame deletion mutant deficient in TDA biosynthesis wherein TDA production was abolished. Molecular networking demonstrated that other chemical sulphur-containing features, likely related to TDA, were also altered in the secondary metabolome. We found dramatic changes in the physiology of the TDA-deficient mutant, S26�tdaB, compared to the wild type S26. Growth of the two strains were similar; however, S26�tdaB cells were shorter and more motile. Transcriptome and proteome profiling revealed an increase in expression of genes and relative abundance of proteins related to a type IV secretion system, a prophage, and a gene transfer agent (GTA) in S26�tdaB. All these systems may contribute to horizontal gene transfer (HGT), which may facilitate fast adaptation to novel niches. We speculate that, once a TDA-producing population has been established in a new niche, the accumulation of TDA acts as a signal of successful colonization, prompting a switch to a sessile lifestyle. This would lead to a decrease in motility and the rate of HGT, whilst filamentous cells could form the base of a biofilm. In addition, the antibiotic properties of TDA may inhibit invading competing microorganisms.
2023-01-01 | PXD035448 | Pride
Project description:Rheumatoid arthritis (RA) and periodontitis (PD) are chronic inflammatory diseases that appear to occur in tandem. Autoantibodies against citrullinated peptide antigens linked pathogeneses with PD preceding RA. However, the mutual impact PD exerts on RA and vice versa has not yet been defined. To address this issue, we set up an animal model and analyzed how the prime inducers of citrullination - Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans – differ in their pathogenic potential. Our experimental setup included collagen induced arthritis (CIA) in the mouse, oral inoculation with P. gingivalis or A. actinomycetemcomitans to induce alveolar bone loss and the combination of both diseases in inverted orders of events. Label-free quantitative proteome analysis revealed that P. gingivalis and A. actinomycetemcomitans led to differential expression patterns in the synovial membranes that were reminiscent of cellular and humoral immune responses, respectively. The P. gingivalis and A. actinomycetemcomitans specific signatures in the synovial proteomes suggest a role for oral pathogens in shaping disease subtypes and setting the stage for subsequent therapy response.
2020-12-04 | PXD020397 | Pride