Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative proteomic dataset from oro- and naso-pharyngeal swabs used for COVID-19 diagnosis: detection of viral proteins and host’s biological processes altered by the infection

ABSTRACT: We recovered proteins from SARS-CoV-2 positive and negative oro/naso-pharyngeal swabs, obtained from diagnostic center localized at Institut Pasteur de Montevideo, and performed comparative quantitative proteomic analysis.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Sars Bat Coronavirus

TISSUE(S): Pharyngeal Mucosa

DISEASE(S): Covid-19

SUBMITTER: Analía Lima

LAB HEAD: Rosario Durán

PROVIDER: PXD020394 | Pride | 2020-07-28

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	NEG1.raw	Raw
	NEG1.txt	Txt
	NEG1rep.raw	Raw
	NEG2.raw	Raw
	NEG2.txt	Txt

Items per page:

1 - 5 of 30

Similar Datasets

Nsp1 and Nsp2 interactome and proteome

Project description:The samples represent pulldowns of protein Nsp1 and Nsp2 from SARS-CoV and SARS-CoV2, as well its unfunctional mutants. Additionally, total proteomes of corresponding samples were analyzed.

2022-05-10 | PXD024480 | Pride

Covid Human plasma LC-MS Multiplatform Analyses Reveal Distinct Drivers of Systemic Pathogenesis in Adult Versus Pediatric Severe Acute COVID-19

Project description:The adult data set. The pathogenesis of multi-organ dysfunction associated with severe acute SARS-CoV-2 infection remains poorly understood. Endothelial damage and microvascular thrombosis have been identified as drivers of COVID-19 severity, yet the mechanisms underlying these processes remain elusive. A multiomics approach identified alterations in analytes associated with fluid shear stress-responsive pathways in critically ill COVID-19 adults as compared to non-COVID critically ill adults.

2023-03-06 | PXD040438 | Pride

Comparative proteomic analysis of exoproteome and membrane enriched fractions of PAK and PAK pJN2133 strains

Project description:This work characterizes a P.aeruginosa strain with low levels of c-di-GMP resultant from the overexpression of the phosphodiesterase PA2133. Phenotypic characterization showed that biofilm formation, adhesion to epitheliel cells, and motility are severely impaired in this strain. We applied both, DIGE / MALDI-TOF/TOF and shotgun LC/MS/MS quantitative proteomic analysis to exoproteome and enriched membrane protein fractions. Results from both complementary strategies were in agreement and revealed motility, type III secretion, and chemotaxis to be the main affected processes by PA2133 overexpression. These results are the first to show that flagella synthesis, twitching motility, and chemotaxis are negatively regulated by low c-di-GMP levels in P.aeruginosa and thus confront our current undertsandings of c-di-GMP signalling.

2017-09-05 | PXD004365 | Pride

Gene profiling reveals specific molecular pathways in the pathogenesis of atherothrombosis in Antiphospholipid syndrome, Systemic Lupus Erythematosus and Lupus with Antiphospholipid Syndrome

Project description:The present gene expression array study of comparative gene profile in monocytes from patients with primary Antiphospholipid Syndrome, Systemic Lupus Erythematosus and Lupus with Antiphospholipid Syndrome demonstrates that the gene expression profiling allows the segregation of these highly related autoimmune diseases, with specific signatures explaining the pro-atherosclerotic, pro-thrombotic and inflammatory changes. One hundred and twenty six patients, forty one with APS, thirty one with SAPS and fifty four with SLE, as well as sixty one healthy donors were included in the study. Monocytes were purified from peripheral blood samples (non-monocytes depleting kit, Miltenyi Biotech, Bergisch Galdbach, Germany). Total RNA from monocytes was extracted using TRIzol reagent. RNA quality control was performed in a 2100 Bioanalyzer. Complementary RNAs from 3 APS patients, 3 SAPS patients, 3 SLE patients, and 3 healthy donors were prepared for hybridization in an Agilent G4112F platform (Whole human Genome microarray 44K) using the One-color gene expression system (Agilent technologies).

2014-03-12 | E-GEOD-50395 | biostudies-arrayexpress

Proteomic identification of recombinant nucleocapsid N protein 40 kDa fragment from SARS-CoV-2

Project description:Serological testing is important methodfor diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Nucleocapsid (N) protein is the most abundant virus derived protein and strong immunogen. We aimed to find its efficient, low-cost production. SARS-CoV-2 recombinant fragment of nucleocapsid protein (rfNP; 58-419 aa) was expressed in E. coli in soluble form, purified and characterized biochemically and immunologically. Purified rfNP has secondary structure of full-length recombinant N protein, with high percentage of disordered structure (34.2 %) and of β-sheet (40.7 %). rfNP was tested in immunoblot using sera of COVID-19 convalescent patients. ELISA was optimized with sera of RT-PCR confirmed positive symptomatic patients and healthy individuals. IgG detection sensitivity was 96% (47/50) and specificity 97% (67/68), while IgM detection was slightly lower (94% and 96.5%, respectively). Cost-effective approach for soluble recombinant N protein fragment production was developed, with reliable IgG and IgM antibodies detection of SARS-CoV-2 infection.

2021-02-17 | PXD023341 | Pride

The landscape of the SARS-CoV-2 HLA-peptidome

Project description:The human leukocyte antigen (HLA)-bound-viral antigens, serve as an immunological signature that can be selectively recognized by T cells. As viruses evolve by acquiring mutations, it is essential to identify a range of viral presented antigens. Utilizing HLA-peptidomics we Identified SARS-CoV-2-derived peptides presented by highly prevalent HLA Class-I (HLA-I) molecules using infected cells as well as overexpression of SARS-CoV-2 genes. We found 26 HLA-I peptides and 36 HLA class-II (HLA-II) peptides, which are estimated to be presented by at least one HLA allele in 99% of the world population. Among the identified peptides were recurrently presented HLA-I peptides, peptides derived from out-of-frame-ORFs and presentation-hotspots. Seven of these peptides were previously shown to be immunogenic, and we identified two novel immuno-reactive peptides using HLA-multimer staining. These results may aid the development of the next generation of SARS-CoV-2 vaccines based on viral-specific-presented antigens that span several of the viral genes.

2021-06-28 | PXD025499 | Pride

CLL exosomes - S100-A9 protein in exosomes from chronic lymphocytic leukemia cells promotes NF-κB activity during disease progression

Project description:CLL exosomes purification during disease evolution from different patients

2017-06-19 | PXD005941 | Pride

Tks5 protein Interactome

Project description:Tks5 (SH3PXD2A) is essential for the formation of invadopodia – specialized membrane microdomains that are essential for breast cancer cell migration in extracellular matrix (mostly collagen type I) and invasion. Tks5 is a large scaffold protein and its function at invadopodia is believed to come from its interaction with other proteins. This project aimed at studying interacting partners of Tks5 and their role in invadopia formation and function.

2020-07-08 | PXD011632 | Pride

Proteome remodeling in the Mycobacterium tuberculosis PknG knockout: molecular hints for the role of this kinase in cell envelope biogenesis and hypoxia.

Project description:Tuberculosis, a pulmonary disease caused by the etiological agent Mycobacterium tuberculosis, is the leading cause of death by a single infectious agent among human beings. One of M. tuberculosis's pathogenic hallmarks is its ability to persist in a dormant state in the host for long periods, reinitiating the infectious cycle when favorable environmental conditions are found. Thus, it is not surprising that this pathogen has developed different mechanisms to withstand the stressful conditions found in the host. In particular, the Ser/Thr protein kinase PknG has gained special relevance since it regulates nitrogen metabolism and facilitates bacterial survival inside macrophages. Nevertheless, the molecular mechanisms underlying these effects are far from being elucidated. To further investigate these issues, we performed quantitative proteomics analyses of protein extracts from M. tuberculosis H37Rv and a mutant derivative lacking PknG. Our results show that in the absence of PknG the mycobacterial proteome was remodeled since 6.5% of the proteins encoded by M. tuberculosis presented significant changes in its relative abundance when compared to the wild-type strain. The main biological processes affected by PknG deletion were the biosynthesis of cell envelope components and the response to hypoxic conditions. Altogether, the results presented here allow us to postulate that PknG regulation of bacterial fitness to stress conditions in host macrophages might be an essential mechanism underlying its reported effect on intracellular bacterial survival.

2021-06-02 | PXD023975 | Pride

Embryonic developmental arrest in the annual killifish Austrolebias charrua: a proteomic approach to diapause III.

Project description:Diapause is a reversible developmental arrest faced by many organisms in harsh environments. Annual killifish present this mechanism in three possible stages of development. Killifish are freshwater teleosts from Africa and America that live in ephemeral ponds, which dry up in the dry season. The juvenile and adult populations die, and the embryos remain buried in the bottom mud until the next rainy season. Thus, species survival is entirely embryo-dependent, and they are perhaps the most remarkable extremophile organisms among vertebrates. The aim of the present study was to gather information about embryonic diapauses with the use of a “shotgun” proteomics approach in diapause III and prehatching Austrolebias charrua embryos. Our results provide insight into the molecular mechanisms of diapause III. We detected a diapause-dependent change in a large group of proteins involved in different functions, such as metabolic pathways and stress tolerance, as well as proteins related to DNA repair and epigenetic modifications. Furthermore, we observed a diapauseassociated switch in cytoskeletal proteins. This first glance into global protein expression differences between prehatching and diapause III could provide clues regarding the induction/maintenance of this developmental arrest in A. charrua embryos. There appears to be no single mechanism underlying diapause and the present data expand our knowledge of the molecular basis of diapause regulation. This information will be useful for future comparative approaches among different diapauses in annual killifish and/or other organisms that experience developmental arrest.

2021-05-12 | PXD025196 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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