Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-resolution proteomics of Zika and Dengue serum samples

ABSTRACT: We used data independent acquisition (DIA) mass spectrometry (MS) to profile ~800 proteinsfrom 122 serum samples Dengue or Zika Trinidadian patients. Two time points were collectedper patient. The DIA MS data were matched against a spectral library generated from high pH/low pH separated pooled serum samples.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Serum

DISEASE(S): Dengue Disease,Zika Fever

SUBMITTER: Shuvadeep Maity

LAB HEAD: Christine Vogel

PROVIDER: PXD015422 | Pride | 2021-03-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

New Proteomic Signatures to Distinguish Between Zika and Dengue Infections.

Allgoewer Kristina K Maity Shuvadeep S Zhao Alice A Lashua Lauren L Ramgopal Moti M Balkaran Beni N BN Liu Liyun L Purushwani Savita S Arévalo Maria T MT Ross Ted M TM Choi Hyungwon H Ghedin Elodie E Vogel Christine C

Molecular & cellular proteomics : MCP 20210212

Distinguishing between Zika and dengue virus infections is critical for accurate treatment, but we still lack detailed understanding of their impact on their host. To identify new protein signatures of the two infections, we used next-generation proteomics to profile 122 serum samples from 62 Zika and dengue patients. We quantified >500 proteins and identified 13 proteins that were significantly differentially expressed (adjusted p-value < 0.05). These proteins typically function in infection an ...[more]

PMID: 33582300

Similar Datasets

Proteomic signatures of the serological response to flu vaccination in a large human cohort study

Project description:This project investigates the serum proteomic signatures of the serological response to flu vaccination. We profiled the serum proteome of 160 flu vaccine recipients from a cohort study conducted in 2019-2020 season, with DIA-MS based proteomics. We compared the protein level between low and high responders based on the response measure seroconversion, as well as the adjusted seroconversion which excludes the confoudning effects of all the semographic factors recorded for these participants. We did the analysis for the composite seroconversion as well as for the individual strains. We also investigated the complex impact of age.

2022-11-17 | PXD036718 | Pride

Serum proteomics in a cohort of COVID patients and healthy controls

Project description:This project investigates the serum proteome patterms in recovered COVID patients compared to that in healthy controls. Specifically, serum saamples from 29 recovered patients and 29 age, sex, and race matched healthy controls were collected and subject to DIA-MS proteomics. A fraction of the serum from each sample was pooled for all 58 samples and run as a quality control.

2024-01-03 | PXD036597 | Pride

Kinome-wide shRNA screen for synthetic lethality in patient-derived FANCA-deficient fibroblasts.

Project description:The purpose of this screen was to identify synthetic lethal targets in FANCA-deficient cells.

2021-05-24 | E-MTAB-9802 | biostudies-arrayexpress

Molecular Remodeling of Ion Channels in Human Atrial and Ventricular Myocytes Associated with Ischemic Cardiomyopathy

Project description:Ischemic cardiomyopathy (ICM) leads to congestive heart failure and can cause sudden cardiac death due to arrhythmia. Existing molecular knowledge base of ICM is rudimentary because of lack of specific attribution to cell type and function. This study was designed to investigate cell-specific molecular remodeling of ion channels, exchangers and pumps, which are signaling molecules (SM) involved in electrical, signaling and mechanical functions of the heart. Atrial and ventricular myocytes were isolated by laser-capture microdissection from left atrium and ventricle of healthy and ICM human hearts. SM and their splice variants altered by ICM in cardiomyocytes were identified by splice microarray and validated by RT-PCR. Molecular profiling of ICM-related changes showed that SM in atrial and ventricular myocytes remodel following their unique programs. ICM affected 63 genes in ventricular myocytes and 12 genes in atrial myocytes. Only few of the identified genes were previously linked to human cardiac disfunctions. In our experiments we used 3 healthy hearts rejected from transplantation procedure and explanted ICM hearts from three male patients. Tissue samples were dissected from left ventricle and left atrial appendages. Atrial and ventricular myocytes were laser-capture microdissected from serial 7-8-Âµm thick cryostat sections. Individual cellular total RNA samples were analyzed on custom-built Human Ion Channel Splice Arrays slides (ExonHit) manufactured on the Ion Channel Splice Array sv1.1 platform representing 287 human SM, including 248 alternatively spliced ones in total 1655 splicing events and supplemented with capabilities to recognize connexins and ryanodine receptors.

2010-05-14 | E-GEOD-17294 | biostudies-arrayexpress

Yme1l substrate quantification under Leucine and Glutamine starvation as well as Torin treatment

Project description:Metabolic reprogramming of mitochondria occurs during development, cell differentiation and in cancer and is coupled to changes in mitochondrial mass and shape. Here, we demonstrate that the i-AAA protease YME1L rewires the proteome of pre-existing mitochondria in response to hypoxia or nutrient starvation. Inhibition of mTORC1 induces a lipid signalling cascade via the phosphatidic acid phosphatase LIPIN1, which decreases phosphatidylethanolamine levels in mitochondrial membranes and promotes proteolysis. YME1L degrades mitochondrial protein translocases, lipid transfer proteins and metabolic enzymes to acutely limit mitochondrial biogenesis and support cell growth. YME1L-mediated mitochondrial reshaping ensures spheroid and xenograft growth of pancreatic ductal adenocarcinoma (PDAC) cells. Similar mitochondrial proteome changes occur in tumor tissues of PDAC patients, suggesting that YME1L is relevant to the pathophysiology of specific solid tumors. Our results identify the mTORC1-LIPIN1-YME1L axis as a novel post-translational regulator of mitochondrial proteostasis at the interface

2019-08-21 | PXD014405 | Pride

Profiling the proteomic inflammatory state of human astrocytes using DIA mass spectrometry

Project description:In the present study we used DIA MS to characterize the profile of over 4,000 proteins in immortalized human astrocytes exposed to TNF, IL-1β, and LPS, as well as in primary human astrocytes cocultured with brain endothelial cells and exposed to LPS. For both immortalized and primary astrocytes, DIA MS data were matched against a spectral library generated by merging DDA MS runs from both unfractionated and fractionated cell lysates.

2018-12-10 | PXD009891 | Pride

Constitutional Trisomy 8 Mosaicism as a Model for Epigenetic Studies of Aneuploidy (DNA methylation)

Project description:To increase our understanding of epigenetic patterns associated with aneuploidy we used constitutional trisomy 8 mosaicism as a model, enabling analyses of single cell clones, harboring either trisomy or disomy 8, from the same patient. We profiled gene and miRNA expression as well as genome-wide and promoter specific DNA methylation and hydroxymethylation patterns in trisomic and disomic fibroblasts, using microarrays and methylated DNA immunoprecipitation. comparison of trisomy 8 cells with disomic as well as reference fibroblasts

2012-12-01 | E-GEOD-40317 | biostudies-arrayexpress

Molecular remodeling of ion channels, exchangers and pumps in atrial and ventricular myocytes in ischemic cardiomyopathy: left ventricle DCM

Project description:We wanted to see whether the set of affected genes in ischemic cardiomyopathy (ICM) is the same or different as compared to dilated cardiomyopathy (DCM). To find this out, we placed the single DCM sample on the same microarray slide with the ICM samples. Analysis of microarray data with ICM samples only showed 63 affected genes, while that carried out with 2 ICM samples PLUS one DCM sample reduced this number to just four genes. From this result we conclude that ICM and DCM affect different sets of genes in ventricular myocytes. Keywords: Expression profiling by array From the associated publication: To find out whether the splice microarray results reported in Table 3 are disease-type specific, we supplemented the same splice microarray of ICM ventricular myocytes with one additional sample prepared from left ventricle of a 41-years old dilated cardiomyopathy male donor. The top-list ANOVA gene score annotation for combined altered CE&P genes in ventricular myocytes (Table 3) was reduced from 63 to just 4 genes (FXYD1 (Gfold = +2.4), HCN2 (-1.5), GLRA1 (-1.8) and GJC1 (-2.3)).

2010-06-17 | E-GEOD-17530 | biostudies-arrayexpress

Extracellular vesicles isolated from human induced pluripotent stem cell-derived neurons contain a transcriptional network

Project description:Healthy brain function is mediated by several complementary signalling pathways, many of which are driven by extracellular vesicles (EVs). EVs are heterogeneous in both size and cargo and are constitutively released from cells into the extracellular milieu. They are subsequently trafficked to recipient cells, whereupon their entry can modify the cellular phenotype. Here, in order to further analyse the mRNA and protein cargo of neuronal EVs, we isolated EVs by size exclusion chromatography from human induced pluripotent stem cell (iPSC)-derived neurons. Electron microscopy and dynamic light scattering revealed that the isolated EVs had a diameter of 30-100 nm. Transcriptomic and proteomics analyses of the EVs and neurons identified key molecules enriched in the EVs involved in cell surface interaction (integrins and collagens), internalisation pathways (clathrin- and caveolin-dependent), downstream signalling pathways (phospholipases, integrin-linked kinase and MAPKs), and long-term impacts on cellular development and maintenance. Overall, we show that key signalling networks and mechanisms are enriched in EVs isolated from human iPSC-derived neurons.

2020-08-20 | E-MTAB-8254 | biostudies-arrayexpress

High accuracy gene expression profiling of sorted cell subpopulations from breast cancer PDX model tissue

Project description:Data sets from 2 experiments using PDX derived human TNBC tissue to compare gene expression between cell subpopulations with distinct marker profiles. The first experiment describes comparison of CD184hi vs. CD184lo population, the second experiment (with a different mouse model) compares CD49f lo vs. CD49fhi as well as CD133lo vs. CD133hi. Each subpopulation shows distinct expression patterns suggestive of distinct function within breast cancer tissue.

2020-08-20 | E-MTAB-9428 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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