Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Filtered Variant Calls After December 2022 (VEO SARS-CoV-2 Taskforce)

ABSTRACT: This project holds the filtered variant calls for the SARS-CoV-2 analysis of public data by the VEO SARS-CoV-2 Taskforce

INSTRUMENT(S): -

ORGANISM(S): Severe Acute Respiratory Syndrome Coronavirus 2

SUBMITTER: EMBL-EBI

PROVIDER: PRJEB57993 | EVA | 2022-12-09

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	2023_03_08_21_31_13.accessioned.vcf	Other
	2023_03_08_21_31_13.accessioned.vcf.gz	Vcf
	2023_03_08_21_31_13.accessioned.vcf.gz.csi	Vcf
	2023_03_08_22_31_08.accessioned.vcf	Other
	2023_03_08_22_31_08.accessioned.vcf.gz	Vcf

Items per page:

1 - 5 of 138

Similar Datasets

SARS-CoV-2 Filtered Variant Calls (COVID-19 Taskforce VEO)

Project description:Filtered variant calls of public SARS-CoV-2 reads

| PRJEB45554 | ENA

hMPXV Filtered Variant Calls (VEO Taskforce)

Project description:Filtered variant calls of public MPXV reads

| PRJEB55823 | ENA

Filtered Variant Calls From August 2022 to December 2022 (VEO SARS-CoV-2 Taskforce)

Project description:This project holds the filtered variant calls for the SARS-CoV-2 analysis of public data by the VEO SARS-CoV-2 Taskforce

2022-08-11 | PRJEB55355 | EVA

Proteotypic peptides for SARS-CoV-2 variant detection

Project description:The recent SARS-CoV-2 omicron variant presented significant challenges to the global effort to counter the pandemic. SARS-CoV-2 is predicted to remain prevalent in the coming months, making the ability to identify SARS-CoV-2 variants imperative in understanding and controlling the pandemic. The predominant variant discovery method, genome sequencing, is time-consuming, insensitive, and expensive. Liquid chromatography-mass spectrometry (LC-MS) offers an exciting alternative detection modality provided that variant-containing peptide markers become well-established. This study demonstrates the potential to establish SARS-CoV-2 peptide markers by examining amino-acid variant-containing tryptic peptides, their MS fragmentation intensities, and their detection sensitivity in MS experiments. We have synthesized model tryptic peptides from of SARS-CoV-2 variants beta, gamma, delta, and omicron and evaluated their signal intensity, HCD spectra, and reverse phase retention time.

2022-10-12 | PXD033777 | Pride

undefined

Project description:Filtered Variant Calls After December 2022 (VEO SARS-CoV-2 Taskforce)

| PRJEB57993 | ENA

Project description:Filtered Variant Calls After March 2024 (VEO SARS-CoV-2 Taskforce)

| PRJEB74099 | ENA

SARS-CoV-2 Systematic Variant Calling (COVID-19 Taskforce VEO)

Project description:Systematically called variant data of public SARS-CoV-2 reads

| PRJEB43947 | ENA

B cell epitope mapping of SARS-CoV-2 spike vaccinated rabbits

Project description:This experiment aims to profile polyclonal antibody binding profiles in serum from vaccinated animals relative to antibody function in a virus neutralization assay. Rabbits received three vaccinations with a DNA vaccine encoding the spike protein of the SARS-CoV-2 index strain. Serum samples were selected based on a three-tier (low, intermediate, and high) capacity to cross-neutralize SARS-CoV-2 strains with known neutralization resistance. Following normalization of total anti-spike IgG levels, serum of each animal (n=3) were evaluated for antibody binding to 10mer cyclic constrained peptides spanning the entire spike protein and regions with known SARS-CoV-2 variant of concern spike mutations.

2023-08-31 | E-MTAB-13040 | biostudies-arrayexpress

N-linked glycan analysis of native SARS-CoV-2 Delta variant Spike

Project description:The SARS-CoV-2 Delta variant is more contagious than WT and causes severe symptoms.To understand the elevated fusogenicity of Delta, we used LC-MS/MS to characterize the site specific N-linked glycan of spike protein in SARS-CoV-2 Delta variant virions.The glycan analysis revealed increased oligomannose-type glycosylation of native Delta spike over that of the Wuhan-Hu-1 spike.

2023-05-10 | PXD033342 | Pride

Transcriptome profiling of the lungs of K18-hACE2 mice infected with SARS-CoV-2 wild-type strain or beta variant

Project description:Diverse severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged since the beginning of COVID-19 pandemic. We investigated the immunological and pathological characteristics of SARS-CoV-2 beta variant of concern (VOC) compared to the ancestral strain. To investigate a broad spectrum of immunological responses and to determine the underlying mechanisms of differentially expressed cytokines, we analyzed the whole transcriptome of lung homogenates from SARS-CoV-2 ancestral strain- and beta variant-infected mice at 4 and 6 dpi.

2022-08-17 | GSE202998 | GEO

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