Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SARS-CoV-2 detection from clinical samples

ABSTRACT: Shotgun analysis of SARS-CoV-2 clinical samples previously characterized by RT-PCR.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Homo Sapiens (human) Severe Acute Respiratory Syndrome Coronavirus 2

TISSUE(S): Nasopharynx Epithelium

SUBMITTER: VALDEMIR CARVALHO

LAB HEAD: Valdemir Melechco Carvalho

PROVIDER: PXD025214 | Pride | 2021-04-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	POOLNEG-01.raw	Raw
	POOLNEG-02.raw	Raw
	POOLNEG-03.raw	Raw
	POOLNEG-04.raw	Raw
	POOLNEG-05.raw	Raw

Items per page:

1 - 5 of 14

Publications

Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts.

Cardozo Karina Helena Morais KHM Lebkuchen Adriana A Okai Guilherme Gonçalves GG Schuch Rodrigo Andrade RA Viana Luciana Godoy LG Olive Aline Nogueira AN Lazari Carolina Dos Santos CDS Fraga Ana Maria AM Granato Celso Francisco Hernandes CFH Pintão Maria Carolina Tostes MCT Carvalho Valdemir Melechco VM

Nature communications 20201203 1

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 9 ...[more]

PMID: 33273458

Similar Datasets

DNA-seq of an ELMSeq reporter cassette to study impact of C-terminal sequence variations on protein abundance

Project description:A ELMSeq reporter cassette was created to monitor Dam levels by methylation, and introduced in the genome. The regions of 6 nt upstream and 6 nt downstream the stop codon were randomized to study their effect on gene expression. The ELMSeq reporter cassette was composed of: promoter - dam - random N6 - stop codon TAA - random N6 - spacer - 4xGATC. The amplicon was spanning the C-terminal region. The cassette was introduced in Mycoplasma pneumoniae.

2020-05-04 | E-MTAB-8223 | biostudies-arrayexpress

ChIP-seq of Atlantic salmon (Salmo salar) gill exposed to varying winter length

Project description:The experiment is designed to assess the impact of winter length on epigenetic status of key genes related to smoltification. Transferring fish from constant light (LL) to short photoperiod (SP) for different durations and then returning to constant light (LL) for 8 weeks to stimulate smoltification. Three histone marks were assessed: H3K4me3, H3K27me3 and H3K27ac.

2023-10-27 | E-MTAB-11091 | biostudies-arrayexpress

Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to Interferon induction

Project description:Adenosine deaminase acting on RNA 1 (ADAR1), is an enzyme that catalyzes the conversion of adenosine to inosine in double-stranded RNA, a process critical for regulation of innate immune response and distinguishing between ‘self and non-self RNA’. It is expressed as two isoforms: nucleolar p110 and cytoplasmic, interferon (IFN)-inducible, p150. The interactome of the p110 under steady-state conditions is well-studied; however, less is known about the interactions of the p150 isoform, particularly during IFN response. To elucidate ADAR1's protein interactions during IFN stimulation, alongside steady-state conditions, three distinct methods of enrichment were used followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). These included: immunoprecipitation (IP) of endogenous ADAR1, IP of Strep II-tagged ADAR1, and proximity labeling using BioID. Individual ADAR1 isoforms (p110 and p150) and their respective dsRNA binding-deficient mutants were created to discern isoform-specific and dsRNA-dependent interactions. Altogether, our results reveal a comprehensive ADAR1 interaction map, identifying both known and novel partners, and highlighting the isoform-specific and dsRNA-binding-dependent nature of ADAR1 interactions. Under IFN stimulation, ADAR1's interaction spectrum encompasses viral replication inhibitors and LINE-1 regulators. Mimicking viral infection with HMW poly(I:C) changed the proximal network of proteins for both isoforms. Our findings provide new insights into ADAR1's roles and its dynamic during IFN response.

2024-12-08 | PXD049991 | Pride

Detection of Lactococcus lactis contamination in standard and ethanol-washed casein used in mouse diets for microbiome studies

Project description:Casein is a common source of dietary protein in defined diets used to investigate the effect of diet on the gut microbiota. Previously it has been shown that the metagenomes of mice fed with a diet containing casein were contaminated with DNA from the bacterium Lactococcus lactis and that washing the casein with ethanol removed this contamination (https://doi.org/10.1016/j.chom.2019.06.013). We have identified the same phenomenon when identifying proteins from mouse diets with casein However, in contrast to DNA sequencing we did not see a reduction in L. lactis contamination in proteomes. Two lots each of standard casein and ethanol-washed casein were analyzed using proteomics.

2024-12-18 | PXD040649 | Pride

scRNA-seq of index-sorted myeloid and lymphoid progenitor cells and differentiated pDCs

Project description:Nine different cell types (common dendritic progenitor (CDP), pre-conventional dendritic cell (pre-cDC), common dendritic progenitor (CDPr, according to Rodrigues et al., but this population was flawed in sorting purity), Flt3+ CD11c+ Siglec-H+ CCR9-low B220-low progenitor cell (lo-lo), Flt3 + CD11c+ Siglec-H+ CCR9-low B220-high progenitor cell (lo-hi), plasmacytoid dendritic cell (pDC), Ly6D+ lymphoid progenitor (SP), Ly6D+ Siglec-H+ lymphoid progenitor (DP) and common lymphoid progenitor (CLP)) were sorted to allow for analysis of their transcriptomic relation and/or similarity. The pDC_precursor_scvelo.h5ad file is a processed file ready for direct downstream analysis with scvelo.

2022-05-21 | E-MTAB-11752 | biostudies-arrayexpress

Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to Interferon induction

Project description:The RNA editing enzyme ADAR1, is essential for correct functioning of innate immune responses. The ADAR1p110 isoform is mainly nuclear and ADAR1p150, which is interferon inducible, is predominately cytoplasmic. Using three different approaches, co-IP with endogenous ADAR1, and Strep-tag co-IP and BioID with individual ADAR1 isoforms, a comprehensive interactome was generated during both homeostasis and the IFN response. Both known and novel interactors and editing regulators were identified. Nuclear proteins were detected as stable interactors with both ADAR1 isoforms. In contrast, BioID identified distinct protein networks for each ADAR1 isoform, with nuclear components observed with ADAR1p110 and components of cytoplasmic cellular condensates with ADAR1p150. RNase A digestion distinguished between distal and proximal interactors, as did a dsRNA-binding mutant of ADAR1 which demonstrated the importance of dsRNA binding for ADAR1 interactions. IFN treatment did not affect the core ADAR1 interactomes but resulted in novel interactions, the majority of which are proximal interactions retained after RNase A treatment. Short treatment with HMW poly(I:C) during the IFN response resulted in dsRNA-binding-dependent changes in the proximal protein network of ADAR1p110 and association of the ADAR1p150 proximal protein network with some components of antiviral stress granules.

2024-12-08 | PXD056080 | Pride

Microarray for transcript expression comparison of normal and Sox18 dominant negative dermal spheres.

Project description:The experiment was designed to identify differential gene expression due to dominant negative mutation of the Sox18 gene in the ragged Opossum spontaneous mouse mutant. Gene expression was analysed after whole RNA isolation in dermal spheres as hair follicle inductive mesenchyme tissue, and was intended to identify gene expression patterns associated with alteration of hair induction post Sox18 mutation.

2017-05-16 | E-MTAB-5673 | biostudies-arrayexpress

MOF-mediated PRDX1 acetylation regulates inflammatory macrophage activation

Project description:Macrophage activation undergoes signal-transduced changes in protein modifications, enabling the coordinated control of transcription and cellular metabolism. However, the role of protein acetylation in signal transduction during macrophage activation remains obscure. Here, we demonstrate that peroxiredoxin 1 (PRDX1), a key regulator of redox signaling, is a novel substrate of the MOF lysine acetyltransferase. Employing a gel based in vitro HAT assay followed by LC-MS, we mapped PRDX1 lysine acetylation sites. PRDX1 K197ac was identified as the most prominent MOF acetylation site. We show that MOF-dependent acetylation of lysine 197 of PRDX1 (PRDX1 K197ac) enhances its peroxidase activity. We find that PRDX1 K197ac is an inflammatory signal-regulated modification, which decreases in mouse macrophages stimulated with bacterial lipopolysaccharides (LPS) but not with IL-4 or IL-10. LPS-induced decrease of PRDX1 K197ac elevates cellular ROS accumulation and augments phosphorylation of ERK1/2 but not p38 or AKT phosphorylation. Concomitantly, diminished PRDX1 K197ac stimulates glycolysis, potentiates H3 serine 28 phosphorylation, and ultimately enhances the production of pro-inflammatory mediators such as IL-6. Collectively, our findings uncover a regulatory role for redox protein acetylation during inflammatory macrophage activation through modulating signal transduction and coordinating metabolic and transcriptional programs.

2024-10-25 | PXD046284 | Pride

Single-cell RNA sequencing of human steady-state immune cells from the lamina propria of colon and matching mesenteric lymph nodes

Project description:The human colon contains an extensively diverse microbial ecosystem and one of the most numerous communities of immune cells. Studies have highlighted dynamic crosstalk between immune cells and commensals. While studies have demonstrated increasing diversity of microbiota from stomach to stool, whether and how immune cell heterogeneity and microbiota diversity change across the colon is undefined. Furthermore, whether these changes are co-depended in the healthy colon is unknown. Here, tissue samples are collected from caecum, transverse colon, sigmoid colon and mLN of cadaveric donors by the Cambridge Biorepository of Translational Medicine (CBTM). We use single cell RNA sequencing (10X genomics) to assess the dynamics of immune cell populations across the colon and in matching lymph nodes. Associated microbiome 16S sequencing data is available.

2020-01-01 | E-MTAB-8007 | biostudies-arrayexpress

RIL-seq analysis of MG1655 Escherichia coli experiencing long-term nitrogen starvation in Gutnick minimal media

Project description:RNA interaction by ligation and sequencing (RIL-seq) was carried out to compare the Hfq-RNA-RNA interactome of MG1655 E coli bacteria that grown in Gutnick minimal media. Wild-type and hfq::3xFLAG tagged K12 E.coli were grown in Gutnick minimal media with 3mM NH4Cl as the sole nitrogen source, and cell samples were taken during exponential growth (N+), ~20min following N-runout and induction of growth arrest (N-), 24hr following N-runout and induction of growth arrest (N-24) and 2hr following addition of NH4Cl to N-24 cells (N-24+2). All sampling was performed in triplicate for each strain and condition

2023-12-01 | E-MTAB-13403 | 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