Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Trypanosoma cruzi Antigen and Epitope Atlas: changes in antibody levels over time in Chagas disease patients from the E1224 clinical study

ABSTRACT: These assays analyze the dynamics of the antibody responses in selected Chagas disease patients from the E1224 clinical trial (ClinicalTrials.gov ID: NCT01489228). The assays measure specific antibody-binding to 392,299 short peptides derived from Trypanosoma cruzi, spanning antigenic regions and epitopes from two different strains of the parasite (CL-Brener and Sylvio X10). The peptides were displayed as short, overlapping sequences in a tiling array format and were assayed with serum samples obtained at three different time points: Time zero (TMZ) = Recruitment; Day 65 (D65) = End of Treatment; Month 12 (12M) = End of followup. Sectorized peptide arrays (QX12-plex slides, Roche Nimblegen) were incubated with primary antibodies, washed and then incubated with fluorophore-conjugated secondary anti-human antibodies. All samples from the same patient were assayed in the same microarray slide, in separate sectors. In total, 108 samples were analyzed, corresponding to these three time points from each of the 36 selected patients. Each sample was assayed in duplicate, with duplicates performed on different slides. A total of 18 arrays (216 sectors) were used.

ORGANISM(S): Homo sapiens

SUBMITTER: Fernan Aguero

PROVIDER: E-MTAB-17293 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Human cerebrospinal fluid proteoform profiling

Project description:. In this study, we have investigated the capacities of last-generation Ultra-High Resolution Q-Tof systems to deal with high complexity intact protein samples, have developed the tools to process the intact protein data in an existing label-free quantification pipeline, and have evaluated the approach on a cohort of patients suffering from neurodegenerative disease in a proof-of concept study. Several proteoforms have been pointed out for their capacity to distinguish Alzheimer disease patients from patients suffering from other neurodegenerative disease and have been characterized.

2018-04-05 | PXD005314 | Pride

The Trypanosoma cruzi Antigen and Epitope Atlas: fine characterization of antibody specificities in human Chagas Disease patients across human populations

Project description:These assays represent antibody-binding assays to analyze seroprevalence of antigens and epitopes at the individual level and also to perform fine epitope mapping characterizations. In this screening 392,299 peptides derived from reactive (antigenic) regions of Trypanosoma cruzi proteins were displayed in the form of short peptides (tiling array, overlapped) and assayed with individual serum samples (antibodies) from Chagas Disease patients across the Americas. Sectorized peptide arrays (QX12-plex slides, Roche Nimblegen) were incubated with serum samples (primary antibodies), washed, and then incubated with a fluorescently-labeled anti-human IgG commercial antibody (secondary antibodies). Raw readouts of fluoresence (signal), as well as normalized signal values are provided in this submission for all samples analyzed. All samples were analyzed in duplicate (r1 = replicate 1; r2 = replicate 2).

2022-08-20 | E-MTAB-11655 | biostudies-arrayexpress

The Trypanosoma cruzi Antigen and Epitope Atlas: discovery of antibody specificities in human Chagas Disease patients across human populations

Project description:These assays represent an antigen discovery screening, and epitope mapping characterization. In this screening two complete proteomes from Trypanosoma cruzi, from two different strains (CL-Brener, Sylvio X10), were displayed in the form of short peptides (tiling array, overlapped) and assayed with pooled serum samples (antibodies) from Chagas Disease patients and matched negative (healthy) subjects selected from 6 geographic regions across the Americas. Peptide arrays (slides) were incubated with pooled serum samples (primary antibodies), washed, and then incubated with a fluorescently-labeled anti-human IgG commercial antibody (secondary antibodies). Raw readouts of fluoresence (signal), as well as normalized signal values are provided in this submission for all samples analyzed. All samples were analyzed in duplicate.

2022-08-20 | E-MTAB-11651 | biostudies-arrayexpress

n-Dodecyl-β-D-maltopyranoside (DDM)-Assisted Resolubilization Enhances S-Palmitoylation Proteomics

Project description:This study demonstrates that adding the non-ionic surfactant n-dodecyl-β-D-maltopyranoside (DDM) during protein resolubilization improves the identification of hydrophobic peptides and proteins in bottom-up proteomics. DDM's effectiveness in overcoming the challenge of losing hydrophobic proteins after precipitation from strong detergent lysis buffers was investigated. Using immortalized mouse macrophages (IMMs), DDM (0.05% or 0.1%) to resolubilization buffers, both with and without 8M urea in 50 mM ammonium bicarbonate (ABC) were added, for global and acyl-biotin exchange (ABE) proteomics (targeting S-palmitoylation). Key findings revealed that the addition of 0.1% DDM increased the identification of total peptides, proteins, and especially membrane-associated proteins in global proteomics compared to urea alone. Gene Ontology (GO) analysis showed that proteins uniquely identified with DDM were enriched in critical cellular processes. In ABE proteomics, 0.1% DDM enhanced the identification of hydrophobic and candidate S-palmitoylated peptides. DDM also increased the number of ABE-enriched proteins, with those uniquely identified by DDM being involved in cellular transport and localization known functions of S-palmitoylated proteins. In conclusion, incorporating DDM during protein resolubilization is a simple and effective method to enhance the coverage of hydrophobic proteomes in various bottom-up proteomics applications.

2025-12-16 | PXD068353 | Pride

Ultrasonic-based OCT-removal from solid tumor biopsies.

Project description:A new method for proteomic studies of OCT-embedded samples based on ultrasound energy is proposed. The cleaning of OCT from mouse kidney embedded tissues were evaluated through the aid of ultrasound energy, with two different frequencies. Simultaneously, vortex agitation was used as control. The optimized method obtained was then applied in human tumor kidney biopsies including chromophobe renal cell carcinomas (chRCC) and renal oncocytomas (RO).

2019-06-13 | PXD013164 | Pride

Proteomics Data of "Integrated Clinical Trial and Molecular Profiling Reveals Immune Drivers of Chronic Hand Eczema" Study

Project description:Background: Chronic hand eczema (CHE) is a debilitating skin condition characterized by pain, itch, and chronic inflammation, with a complex multifactorial origin. Its diverse presentations, including overlapping traits of atopic dermatitis, contact dermatitis, and psoriasis, make diagnosis and treatment particularly challenging. The underlying immune mechanisms of CHE still need to be investigated.Methods: Here we conducted a comprehensive molecular profiling of CHE patients, enrolled without prior selection on etiology and morphology, and performed a phase 2b randomized, multicenter, double-blind, placebo-controlled clinical trial comparing dupilumab to placebo over 16 weeks.Results: We demonstrated that CHE patients may benefit from IL4Rα-blockade, regardless of etiological factors or clinical presentation. Skin transcriptomic and serum profiles of CHE patients closely resemble those seen in both atopic dermatitis and psoriasis, with dysregulated genes affecting keratinocyte differentiation, leucocyte-mediated immunity, cytokine signaling, and mixed type 1, 2, and 3 immunity. The clinical trial included 94 adults with moderate to severe CHE persisting for at least six months and resistant to potent topical corticosteroids. Compared to placebo control, 16-week dupilumab treatment significantly improved clinical severity and quality of life of all CHE patients while largely restoring appropriate transcriptomic and proteomic programs related to skin barrier and immune homeostasis.Conclusion: These findings confirmed the involvement of not only type 2 but also type 1 and type 3 immunity across all CHE patients, and demonstrate that IL-4Rα blockade may offer effective therapeutic perspectives for this highly burdensome condition, independent of an atopic dermatitis background.

2026-02-26 | PXD059218 | Pride

Immunogenic epitopes of the meningioma-associated antigen TXNDC16

Project description:We used customized peptide arrays of 163 TXNDC16 peptides to identify immunogenic TXNDC16 epitopes and asked whether discrimination of meningioma and control sera is possible with a specific subset selection of all immunogenic epitopes. CelluSpotsM-bM-^DM-" peptide arrays were manufactured by Intavis (Germany) with 163 TXNDC16 spanning peptides spotted as two replicate subarrays. 15-mer peptides overlapping by 10 amino acids were covalently bound to cellulose membranes with their C-termini. Please note that the non_normalized.txt contains Ch1 Mean values for all samples (each sequence represented in duplicates) and the identifiers in the 'index' column corresponds to those in the 'index' column in raw gpr files; sample data table contains classification values (for each sequence) described in the sample data processing field.

2014-07-01 | E-GEOD-58949 | biostudies-arrayexpress

Down-regulation of Interferon signature in systemic lupus erythematosus patients by active immunization with Interferon alpha-Kinoid extended follow-up

Project description:Interferon-alpha Kinoid (IFN-K) is a therapeutic vaccine composed of IFN-alpha2b coupled to a carrier protein. In a phase I/II placebo-controlled trial, we observed that IFN-K significantly decreases the IFN gene signature in whole blood RNA samples from SLE patients (see GSE39088). Here, we analyzed extended follow-up data from IFN-K-treated patients, in terms of persistence of neutralizing anti-IFNÂ± Abs, gene expression profiling and safety. Follow-up analyses in six patients confirmed a significant correlation between neutralizing anti-IFNalpha Ab titers and decrease in IFN scores compared to baseline. These analyses also revealed an inhibitory effect of IFNÂ± blockade on the expression of B cell associated transcripts. Extended clinical (SLEDAI, BILAG, Physician Global Assessment) and biological (binding and neutralizing anti-IFNalpha Ab titers, C3 concentrations and anti double-stranded (ds)DNA Ab titers) follow-up data were collected in 6 IFN-K-treated patients. In these patients, whole blood samples were collected in PAXgene Blood RNA tubes (Qiagen) every 6 months after completion of the initial study. RNA was extracted from these samples, and was also re-extracted from baseline (month 0) and day 168 (month 6) PAXgene tubes stored at -80Â° from the same patients, and from 10 healthy volunteers.

2016-02-29 | E-GEOD-72754 | biostudies-arrayexpress

Screening of rheumatoid arthritis patients sera against citrullinated fibrinogen peptides using ImmunoCAP ISAC system

Project description:Citrullinated and unmodified peptides (>95% purity, ProImmune AB) were immobilized onto a chemically modified glass slide, sera from RA patients and healthy controls were applied into the reactions sites and fluorescence intensity after incubation with anti-human IgG antibody was acquired in a laser scanner. Final results for each citrullinated peptide were calculated by subtracting the intensity values of corresponding arginine containing control peptide from citrullinated peptide for all RA patients and controls.

2015-10-25 | E-MTAB-3606 | biostudies-arrayexpress

Comparison of CAP-patients with a severe disease course vs. CAP-patients with non-severe disease course

Project description:Clinical decision-making in patients with community-acquired pneumonia at risk of organ dysfunction and death is currently aided by clinical scores. Here, we compare transcriptomes of patients to identify a signature to better identifie patients-at-risk for ICU admission and death. For this, we analyse time-course transcriptomic data from samples of a prospective observational cohort study that included hospitalized CAP across 63 centers in Germany (‘PROGRESS’; clinicaltrials.gov NCT02782013). This case-control study consisted of discovery (n=240) and validation cohorts (n=215) where transcriptomic data were analyzed for association with a composite endpoint (cEP) of qualified ICU admission and 28-day mortality.

2026-01-31 | E-MTAB-11796 | biostudies-arrayexpress

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